XS650 Top End Buildup


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This thread details the reassembly of the top end of my 1980SG. Everything's already cleaned up and measured, but I'll backtrack a little and show how to do some measurements. All manual references used here are from the 1978-80 Yamaha Service Manual. All points of view (left and right, fore and aft) are referenced to the riders point of view

I'm writing this for anyone who's never done a top end before. If you have, you probably won't learn anything new.... or maybe you will. Keep in mind, this is how "I" do it. If you do something different that will add to the usefulness of this thread, by all means jump into the discussion.

Before we get started, you need to check the big and little ends of your connecting rods. I did this while the bottom end was disassembled and unfortunately, didn't take any pics of it. Pg. 27 of the manual tells you what to check for and the dimensions. You need to do those checks before starting the top end reassembly. If you can't figure out how to do it, bring it up in the comments and I'm sure someone will do some 'splainin'.
Let's get started.

EDIT 3/13/24: The gaskets I used for this are Athena green gaskets. DON'T USE 'EM!! They're little more than junk in my opinion. Have a read here. And read some of the comments after that.

First off: Sealant. I use Permatex Aviation sealant....


The brush inside the cap is a little unwieldy. I use a Q-tip for better control and less mess. I've overhauled or repaired hundreds of engines in my career and this is all I've ever used. It's never let me down. If you prefer Yamabond or some other sealant... then by all means, use what works for you.

Since you already have the top end apart, now would be a good time to replace your stretched out cam chain. Use a piece of safety wire to join the new chain to the old one and work it into place.


Once the chain's through, use some safety wire to tie both ends together and tied to one of the studs. Ya don't wanna lose it back down in the engine... :(

The next thing I did was install the cam chain tensioner. It's a new one from Mikes because I couldn't find an OEM one. I hope I don't come to regret that. There's 2 long and 2 short screws. The long screws go on the right.


The 4 screws are JIS... not phillips. A phillips screwdriver will strip the heads. You can modify a #2 phillips by grinding the point like this.....


I find that this works just as good as a JIS screwdriver. Oh... and I put a little blue Loctite on the screws, then tighten to 85 in.lbs. If you're worried about dropping screws and washers, do it this way....


Next, make sure the two alignment bushings are installed (red arrows) and install the base gasket.


I know some people don't use gasket sealer here, just grease or oil.... I do. Just make sure you get it on the right side/bottom of the gasket so you're not makin' a mess as you go (test fit it if you're not sure. It only fits one way). Make sure you re-secure the cam chain after you slide the gasket down. Rotate the crank so that the connecting rods are up at TDC and secure with rubber bands as shown. This keeps the rods centered as you install the pistons.

OK, on to the cylinders. I like to hone them right away and do all the measuring afterward. Honing knocks the glaze (shine) off the cylinder walls. This gives a scratched surface that aids in ring seating and in oil retention (lubrication). There's tons of videos out there if you've never done it before. Seems everybody has their own techniques and opinions on the best way to hone a cylinder. I've found this short one that does a fair explanation on how to do it.

You can look at some of my pics below to get an idea of what the end result should look like. If you've never done this before, it might be worth getting an old cylinder and practicing first. It's up to you.... If, after honing you still have score marks in the cylinder, you might want to put a good pic of it up in the comments and let the "gurus" here give you their opinion on whether they're acceptable or you need to do an oversize bore job.

Providing the honing process went good, now's a good time to install the big o-rings in the bottom of the sleeves (top arrow) before you forget em.


The bushings for the cam chain guide, technically called guide bar nuts (bottom arrow) have copper crush washers for oil sealing. There's several ways you can go here.... your best bet is to install new ones. Or you can use a torch to anneal them....


All it takes is a propane torch to heat them to a bright orange and then quench them in water (thanks Dick). Don't hold the heat on em' for too long or they'll start to deform/melt on you. Now they're soft again and can be re-crushed into an oil tight seal. Your third choice is to spread a little sealant on the threads and torque em down. any one of these will work just fine for oil sealing. A word of caution here: There were reports in the past of the MikesXS bushings being too long, causing the cam chain guide to stick too far into the cylinder. If you're using aftermarket bushings, measure 'em against the originals and make sure they're the same.

OK, assuming you've got your cylinders all cleaned up, it's time to check them for serviceability. The next thing we're gonna' do is check the bores for excessive wear, roundness and taper. You'll need a telescoping gauge (usually just called a "T" gauge) and either a micrometer or caliper that can measure down to 4 decimal points (this is all written for inches, not metric). I've found that even many seasoned mechanics don't know the correct way to use a T gauge, so I've made a short video showing the correct way to use it.

Your manual (Pg. 26) has the dimensions and tolerances you're looking for and a picture showing where to check. There's 6 places to measure... towards the top, middle, and towards the bottom, then again at 90deg. to the first checks. From these measurements you can determine taper, roundness, and diameter. Write these down.

Now measure measure the piston skirt as shown on Pg 26. I use a wooden block dropped down inside the cylinder to rest the piston on for this check.


This dimension, subtracted from the bore dimension (I use the mid point measurement for this) gives you your skirt clearance dimension. The specs. on Pg. 64 give a skirt clearance of .002" to .0022".

Lets talk about cylinder, piston and ring matching briefly. No two pistons are the same.... no two cylinders are the same... no two rings.... well, you get the picture. Measure both skirts and compare them to both cylinders.... then decide which piston is left and which is right. Think balance..... If one skirt is at the minimum and one at the maximum..... and you swap the pistons and now both are towards the max. but are the same..... Which configuration do you think is better? Exactly... you want balance. Do the same for the rings (next section). Mix and match until you can get the best balance of ring gaps.

An alternate way to check the skirt clearance is to use a feeler gauge.


With the piston pushed to about midway into the cylinder (correctly oriented), a .002 feeler should be a snug fit and a .003 should immediately start to bind up as you insert it. I prefer to use tapered feeler gauges for this, but mine seem to have grown legs...:(


OK, now let's see how flat the face is. You need something absolutely flat and rigid. I use a piece of 7075T6 aluminum angle.


Move it around to various places on the face and see if you can slide a .001 to .002 feeler under it at any point. If you can, you might want to consider refacing it. I'm not gonna cover doing that here, but if you need to do it, bring it up in a comment and I'll (or someone else will) explain how to do a "backyard" refacing.
If all these checks are good, you are now the proud owner of a serviceable set of jugs. :)

I'm guessin' I'm about to hit my character limit on this comment. So, we'll continue below on the next one.
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Still there? Good. Don't put them nice shiny jugs away yet. We need them now to check our piston ring gaps. Take your new rings (I always use new ones) and one piston. One at a time, slip a ring into a cylinder about a third of the way down. Now take a piston and insert it dome first. Push it against the ring to "square" the ring up in the cylinder. Measure the end gap with a feeler gauge. Take the same ring and do the same thing for the other cylinder. Decide which ones left and which is right and organize them appropriately.


Do this for the top, second, and both halves of the oil control ring. The gap clearances are listed on Pg. 27. Remember, the smaller the gaps, the better the seal and the longer the ring life. An old hot rodder trick is to use the next oversize rings and then file/grind the ends 'till the gap is at the minimum value.

Once you're satisfied with your gaps, go ahead and install the rings... starting with the oil ring. Install the spreader ring, then the lower, and then the upper rail rings. Make sure the gaps in the rail rings are opposite (180deg.) each other and the gap in the spreader is about halfway between the two. Even when I'm using ring spreader pliers, I still wrap the grooves with electrical tape so that I don't scratch em'.


Once the oil ring's in, move the tape up and install the second ring..... same for the top one. Take your feeler gauge and check for the ring side clearances listed on Pg. 27.


Now you can either set that piston aside and do the other one, or go ahead and install it in the cylinder. I decided to go ahead and install it. Before you install it, make sure the inboard wrist pin clip is installed. Page 32 shows the correct orientation of the ring gaps. Give the inside of the ring compressor a good coating of oil and tighten it up around the piston. NOTE: If your piston is cocked in the ring compressor, your rings aren't compressed all the way. Tap the bottom of it with a piece of wood a few times and snug it up again.The piston won't go into the cylinder unless the rings are fully compressed.... and could possibly damage the rings and/or piston. Give the inside of the cylinder a good coating of oil, set the piston in the cylinder correctly oriented, and tap it into place. If you're using OEM pistons, there's an arrow on it that points forward. If there's no arrow, just remember that the larger valve pocket (intake) goes aft.




There's several ways you can install the pistons. Keep in mind that at the beginning of this article I stated that this is how "I" do it. I have a good quality ring compressor that's served me well for over 30yrs. I'm comfortable doing it this way. The bottom of the cylinders have a slight bevel and some might feel more comfortable inserting the pistons from the bottom. Because of that bevel, you can literally use a couple pieces of wood to squeeze the rings together and insert the pistons without a compressor (it helps to have 3 hands here...;)). I've done it that way and it works. Do what works best for you with the tooling you have.

Bobs build.jpeg

After you get both pistons installed, tap both of them down (or up) 'till the wrist pins just clear the bottom of the sleeves and are parallel to each other.



Cut 4 pieces of wood 4" long and tape or tie them to the front and rear of each cylinder.


install the cylinder and let the wood rest on the base gasket. Don't forget to pull the cam chain through and tie it off.


With the wood holding the cylinder height and the rubber bands holding the connecting rods centered, you should be pretty close on alignment. Rotate the crank and/or push the rods fore or aft slightly and the wrist pins will slide right in.


Stuff a clean rag in there in case you drop the clips and go ahead and install the outboard clips. Once you're satisfied the clips are properly seated, double check em to make absolutely sure they're seated. Now go ahead and remove the rags, rubber bands, and pieces of wood, then apply a thin bead of sealant around the perimeter of the base gasket. Use your solvent of choice to clean up any mess you made, then work the cylinders down into place.


If your pistons went down to BDC, hold the cylinders and work the cam chain to bring them back to TDC. I do this just to lesson the possibility of accidentally leaving something in the cylinders that don't belong there and because they need to be there for cam timing.

Next I installed the chain guide. The fastener holes are cut more towards one end (top). Slip the longer end down into the cylinder and install the fasteners. Screw the fasteners in by hand till they seat, then back 'em off a hair so you can wiggle the guide around easily. Pull the front of the chain up against the guide and wiggle the chain around until you're certain it's laying inside the guide properly. Eyeball the guide and chain so that you can center it up inside the chain cavity and just snug the bolts down. Watch the guide as you tighten. If you see it move one way or the other, loosen it up and try again. My eyeballs have been doin' this kind of stuff for close to 50 yrs. now. I trust 'em. If your not sure you can judge the center, put a piece of tape across the cavity and mark where the chain and guide should be. The bolts use copper crush washers just like the bushings do. Treat them the same (see above). Once you're happy with everything, go ahead and torque the bolts


This is the XS/SR500 Frankenstein modded guide. You can read about how that was done here. I did manage to score an OEM guide for 115 bucks, but elected to use the modded one so I could see how well it holds up. Time will tell.....
Note: You can just as easily install the guide before you install the cylinder. In fact, some people who know a lot more than me about the XS say that you should install the guide first so that you can measure it top and bottom and make sure it's centered. I'm happy with the way I did it. Obviously, it's your choice as to which way you go, but if you're uncertain... I'd suggest you measure it and install it first.

At this point, I'd normally take the opportunity to put a dial indicator on a piston and verify the TDC mark on the rotor. My rotor's dead and I'm gonna have to replace it. So, instead of doing it twice, I'll check it through a plug hole when the engines back together.

I'm probably gettin' close to my character limit again, so we'll continue below. Next up: The head.


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OK, movin' right along... time to install the head. It's already built up and ready to go. I'm not going to go into any detail on the valve job because if you have all the tooling to do a proper one... then you probably already know how to do one.... and for that matter, how to install it. In which case, you're probably not even reading this... ;) So, we're going on faith here that you sent your head out and had the professionals do it. Don't forget to give the machine shop your new guide seals... else they might assume you want em' to re-use the old ones. Don't ask me how I know that... :(

The alignment bushings go in first (red arrows).


I use Copper spray for the head gasket. It supposedly helps with heat transfer. Not sure if it really does.... but it does get the sealing job done. It's sticky stuff. Spray it in a cardboard box or a garbage can.


Don't forget to invert the can and spray 'till it's clear when you're done, otherwise it clogs the nozzle. Let it dry for 30min. to an hour so all the solvents and propellants evaporate, then place it on the cylinders. It only fits one way. Test fit it before spraying if you're not sure.


Set the head on the top of the studs, pull the chain through, and make sure the chain tensioner is pushed as far forward as it will go. Then lower the head down till the alignment bushings seat. Don't forget to re-tie the chain.


At this point you need to get organized and have everything you need sittin' next to the motor and a very good idea on how you're gonna do it. Read through this section several times and visualize how it's gonna work.

I take a fresh piece of safety wire about a foot long and tie it to both ends of the chain to make one big loop. Pull up on the loop and rotate the crank about a half a turn in both directions. Any links kinked up on the crank sprocket will pop loose and all your chain will be sticking up. Pull the chain one way or the other (keeping the loop pulled tight) until your TDC mark lines back up on the rotor. In fact, from this point on, do not stop pulling up on that loop until I tell ya to stop. Now install the camshaft with the radial notch on the sprocket on the left side of the motor and the punch mark on the right. Align the notch vertically (mentally draw a line through the notch and down through the center of the crank sprocket) and wrap the chain around it. If it's a new chain, be prepared to wrastle that bugger. It'll be a tight fit.
Edit: 5/30/18. If you absolutely can't wrestle the chain in place, here's how @robinc did it. Comment #894


I took this picture after I installed the master link, but it's just to show you what you want to see with the crank at TDC. While still firmly holding the safety wire, look on the other (right) side. The punch mark should be parallel to the head mating surface as shown by the screwdriver tip.


If you're satisfied that you are in fact on the right tooth and your chain ends meet each other with one tooth in between them and the crank is still on TDC, twist the safety wire loop together to hold the chain in place on the sprocket. Now you can let go of that loop. Take a couple of shop rags and a blunt object... and wedge the rags between the chain and the head on both sides of the sprocket.


Wedge 'em in tight so there's no possibility of the chain falling off the sprocket. Now you can remove the safety wire that's been stopping the chain from falling inside the engine. Take a couple more rags and stuff em' down the sides of the sprocket so that when we fumble around and drop a piece of the master link, we ain't gotta figure out how the hell we're gonna fish it out of the bottom of the engine:(


With both halves of the master link in place, I measure the diameter of the link pins prior to riveting.


The ends of the link pins are hollow and the link riveter I have has a nice rounded pin with it. Crank that sucker down....


And you wind up with this.


Makes a nice neat job of it. Measure afterwards. I look for about a .010" flare on the end of the pins. There's tons of homemade tools out there for riveting links, and I'm sure someone will chime in, in the comments on how to make your own and their way of doing it. As long as the pins are flared out so the link plate can't fall off, you're golden. Now you can remove the rags. Go ahead and spin the crank a couple of revolutions just to make sure nothing is jammed or binding. It's a million to one... but best to find it now rather than later when the engine's back in the frame.

Next up, the rocker box. Install the two alignment bushings in the head (red arrows).


Apply sealant sparingly as indicated by the arrows below. Note the double arrows in the front and back of the head. Those holes are drilled through the head to the outside world. Apply sealant all the way around those holes. Squirt some motor oil on the cam chain and into the cam bearings and smear some buildup grease on the cam lobes.


A quick note about the sealant. Permatex says to apply it to both mating surfaces. If I'm assembling right away (10min. or less) I only apply it to one side. After a couple of hrs the sealant will 'tack over'. If that happens, I'll go ahead and put it on both surfaces. You can do it that way or follow the instructions... whatever makes you comfortable. Just keep it thin. Even then you'll get some squeeze out at the seams.

Back the valve adjusters off until they're almost flush with the rocker arms, or just leave 'em out for now. That prevents you having to fight against the cam lobes as you seat the rocker box.
There's 4 sleeves that go into the outboard stud holes. Replace the seals and push 'em up into the rocker box. If they're a snug fit.... great. If not, smear a little assembly grease around them to hold them in place while you lower the box onto the head.



With the valve adjusters backed off, the rocker box should fully seat on the head just by tapping it by hand.

The 4 outboard stud holes have oil pressure running through them in the rocker box and require a sealing washer. OEM washers were rubber coated plain steel. Copper and brass washers are also available. What you use is entirely up to you. Done correctly, any of the three types will work. I used copper because the original rubber ones were trashed and my local hardware store had the coppers for 99 cents each (Mikes wants about three and a half bucks each). So... coppers on the 4 outboard studs and plain steel on the 4 inboards. Install all the nuts and bolts and just lightly snug them up for now. Do not torque them yet!

The next step is to install and tighten the point and advance housing as explained below in the next comment. Once that's done, come back to this section and torque the head fasteners in 2-3 stages per the sequence on pg. 33 of the manual. The correct sequence is also depicted below.
Let's talk lube torque vs. dry torque here for a moment..... there's many a discussion here on the forums about whether to install the head fasteners dry or lubricated. The early XS manuals specifically stated "lubricate all head fasteners with motor oil." The later manuals such as my 78-80 do NOT say to lubricate. Quiet the dilemma huh? An advantage of lube torque is that it's easily repeatable, more accurate and smoother because of the reduced friction in the threads. BUT....... that reduced friction also means that for a given torque, you're loading more tension into the fastener. In some cases, a lot more....as much as 20-40% more tension. Yikes!! :yikes: Add to that the fact that well used fasteners have threads that are more polished because of numerous tightening and loosening cycles... and therefor have less friction to start with, and it becomes obvious why older hardware tends to strip its threads more easily when a lubricant is added.
So.... here's how I do it. I lubricate the fasteners with motor oil and use less than the specified torque. For the studs I went 8ft-lb on the first torque, 16 on the second and a final torque of 27ft-lbs. The bolts got 5, 10 and 14ft-lbs.... and the small bolt at the rear got a snugging on the first go, 36in-lbs on the second torque and a final torque of 72in-lbs.
Note: I used 'inch pounds' on the small bolt. Please don't try and put 72 'foot pounds' into that little bitty thing.


EDIT 5/16/18: The head torque values described here are NOT per the Yamaha manual. It's done my way, based on 50yrs experience turning wrenches for a living. You can do yours any way you see fit. I'm not suggesting or recommending any particular way of doing it.... and certainly not accepting any responsibility if you do it the way I did and screw something up. This works for me. Your mileage may vary....

EDIT 5/22/18: @robinc pointed out to me that I forgot to mention the oil baffle that goes in the back of the head. Don't forget to make sure it's in place before setting the head on the engine. Here's a shot Robin took of an old head.


Here's a handy little trick for ya..... if you're using a TCBros/Mikes style buildup stand and have no one around to hold the engine while you torque it, clamp a piece of wood across the bench and clamp the back of the stand to it.

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Before you torque the head down, you need to install the two covers where the points and advance mechanism go. The flanges on these are what centers the cam and cam bearings in the head. If you torque the head first, these covers probably won't seat properly and your cam and bearings won't be properly centered. EDIT 2/3/19. For the most accurate cam centering, install the housings without the gaskets and o-rings and tighten. Once you're satisfied they're seated, take 'em back off and install them with the gaskets and o-rings. END EDIT.

To replace the camshaft end seals, press them out and back in with a hyd. press if you have one and a socket just slightly smaller than the seal.


If you don't have access to a press, use your vise the same way using the socket and a piece of wood...


As you can see in the next pic, the Tour Max seal kit I used isn't quiet the same as the OEM seals. They're a little thinner.


New is on the left, OEM on the right. Where the OEM was flush on both sides when installed, the new one will be slightly recessed on the outside (red arrow). Just make sure the inside of the seal is flush with the inside flange after pressing in (red arrow in next pic.).


Install the gasket and O-ring.....


.....a drop of blue loctite on the 6 screws (3 per side), and torque the covers into place. Don't forget to add the cone shaped starloc washers to the screws. Not really sure why Yamaha saw fit to use a gasket and O-ring on these...


If you had the rocker arm shafts out, don't forget to reinstall the plugs first. Now you can go ahead and torque the head as described previously.

The oil tube is next. The union/adapter has a crush washer that needs annealing or replacing.


You'll need a 22mm crows foot to properly torque this (a 7/8" SAE will also work). Don't forget to put the crows foot 90deg. to the torque wrench so the torque value doesn't change.


There's two copper crush washers for each banjo bolt.... one between the bolt head and the oil tube and another between the oil tube and the rocker box. Treat them as previously explained.




EDIT 3/21/24: Quick note on the oil tube. they don't usually lay exactly centered on the head. They'll usually favor the left side, in most cases to the point they'll touch the side of the valve cover hole. That can wear through from the vibes. The tubes are copper and bend pretty easily. Just tweak it until you have 3-4mm clearance from the head.
(Image courtesy of Bob @Mailman )


The cam chain tensioner is next. I back the tensioner all the way out and then thread it back in a turn or two.


A light coat of sealant on both sides of the gasket.


And install the tensioner assembly.


Once the tensioner is installed, I adjust it in until the pin is recessed about 1/16" to 1/8" (green arrow). Note: This is just for the initial run. After I'm satisfied everything is good on the run, I'll readjust it per the book. Make sure the copper crush washer (red arrow) is either new or annealed and tighten the lock nut down while holding the adjuster. Install a new o-ring in the acorn cap (red arrow) and install it.


The next step (for me anyway) is to install the engine. Once installed I'll spin it over 'till I get good oil flow showing inside the valve covers. Once I'm happy with that I'll go ahead and adjust the valves and install the valve covers... then the carbs... exhaust.... well, you get the idea. Hope you guys found this helpful.


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If you see obvious problems in this thread, by all means point them out and I'll correct them.... I never claimed to be a tech writer. ;)
I wrote this in the Lab over the course of several weeks, so some of the mistakes have already been pointed out and corrected. There's several links that directly pertain to this thread. Gimmie a few days and I'll get 'em up here.
Thanks to TwoManyXS1Bs, 650skull and gggGary for their valuable input
Edit 10/6/18: Some useful links written by other forum members and provided by the above gentlemen...
Discussion of piston installation (with videos).
Complete engine rebuild.
Discussion on front guide replacement
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Jim, this is beautiful work. I do a few things a little differently, but if the rest of the series is anything like the start, a novice wrench or an old hand who hasn't done many (or any) XS650 motors will find everything he needs to know, including all the little things we take for granted. Admin, this needs to be copied in the Tech section when it's done!
Thanks Griz!
.....including all the little things we take for granted.
Yeah... that's the hardest part of writing something like this.... some of the tricks we learn along the way we take for granted and don't really think to add them.
Yes, very nicely done. I'll just add a couple things ..... I've always centered the cam in the head by measuring and matching the bearing insets on each side. Honestly, I never even thought of using the points/advance housings to do the job but maybe I'll try that next time .....


Also, before torquing I like to loosely fit all 4 valve covers. I just fit them and put the nuts on finger tight. This assures the holes in the head are aligned to the covers and that they don't bind on the studs. I know there are alignment dowels between the head and top cover but there is still the possibility for a small amount of movement or misalignment. I discovered this several years back working on a local guy's bike. I had to do a Helicoil repair on a valve cover stud and apparently it didn't come out 100% straight. That cover bound a little going back on the studs. A year or so later, we did the topend on that motor. Fitting the valve covers before torquing cured that binding cover.

When applying the sealer for the top cover, I go completely around the 4 outside stud holes (like you did on the lower left one in your pic). I also do the little contact rings around the 4 inner studs. I've always found sealer on them from the factory when I take one apart so I follow suit.

I don't follow the factory practice of using sealer on the points/advance housing gaskets. I just oil them up and usually replace the o-ring. If the original red (silicone?) o-ring is in good shape and not deformed, I will re-use it. I found that black replacement all deformed when I removed one of my housings a few years after my rebuild. It had changed from round to square, lol. I'm guessing the heat tolerance of that plain black o-ring (probably Buna-N rubber) isn't good enough for this higher heat area.