Splitting the crankcase

Ok so I'm going to be putting the cases back together soon. On the bottom case around 2 or 3 of the holes that the bolts come through have some powder coat on them, very light but some none the less. What's the best way to prep that and not ruin the case so it still seals?
Hey fellas...splitting the crankcase tonight I hadn't read about backing each nut a quarter turn at a time and I just undid all the nuts....eventually finding 2 I hadn't seen until all the others were undone. What are the chances of having warped the crankcase? Is this puppy gonna piss all over me when I put her together? Slightly worried cos I'm a worrier.
No worries, really. The back the nuts off a 1/4 turn at a time sounds a little OC to me after all the nuts are out getting the cases apart is STILL going to be a project, they are yamabonded together pretty well. Case leaks on XS650s are very rare. Just took apart a set and it was a project getting the halves apart. I like the earlier post about nuts bolts as splitting tools. The ones I did will never be a running engine again (severe damage from a stuck valve event). I used an aluminum drift and a BFH and it took a while to get em apart.
I've split quite a few of these motors and never had any serious grief with separation; a wooden mallet did it for most, a few needed persuasion with a steel hammer and wood drift (short piece of 2X2).
I recently had to split my cases and they would not split after about 2 hours of mallet pounding. I ended up putting my cases in the middle of my truck, attached ratchet tie down straps to the top and bottom engine mount points, then to the corners of my truck and after a few ratchets, they split pretty easy. Wish I would have thought of that sooner.
I also found that using a heat gun at the mating service will loosen up any cement holding the halves together. Apply the heat gun to an area and they start to pry/hit them apart. Worked for me!
I attempted splitting before reading this. I just pulled all the nuts/bilts without regaurd to order. Everything screwed up now or no worries?
No worries! Some guys have OCD that's all.

Heat to split, don't forget the one behind the clutch basket.
Acorn nuts and copper washers must be used in positions 1,2,3,4,12,13.


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So following this I finally got my engine split and have successfully removed everything except this! No idea how to. Anyone?
That is pressed in there. If you're going to take it out you have to weld a bar to the end of it on an angle for leverage and that will allow you to work it out. I left mine in there just cause it was a hassle. You don't need to take it out but that is how.
I have been reading the forums for a few weeks now and decided to tackle my own gear repair!
I have several bikes and have been tinkering with bikes for a couple of years, never done anything more than basic engine removal and replacing brakes, basic maint. and such, never cracked a case or done any internal engine repair.
I thought I would try the 2nd gear repair myself as a noobie and document for all the other noobs that may want to try.
I want to split the case and just take the bottom off and replace second gear.

The engine has low miles and PO took very good care of bike, this is why I want to do this from the bottom.
What should I watch out for, if anything when splitting the case upside down?
I have built a engine stand and plan on pulling the top off and leaving the bottom crank case on the stand.
Do I need to release the cam chain to pull the top off?
I hoped all the other gears will stay in place .
If anybody has any tips or suggestions, many thanks.
Just gotta ask; why do you think the gears for 2nd are bad? While a lot of old Yamahas had "the second gear issue" the XS650 is not in that group. While anything is possible I would want to do the "shift star alignment as found in the manual and several threads on here before I opened the cases.

Take a look here
Hi Gary,
Thanks for the response.

The PO said he was having trouble getting the bike into second gear, he took it to the local yammy dealer and they took the drian plug of and a piece of gear was stuck to the magnet, they said they would have to tear it apart to find out and not to drive it.

I am only assuming it is the second gear because he was having trouble with second, it could be another, but after what the dealership had said and reading thru several post about pieces of metal on drain plug, I am 99% sure its a dog of a gear, dude even showed me the piece.
I found that using tie down straps on table legs and hooked i to the rear motor mounts was an easy way to split the cases.

Also make sure to check your shift forks for bending or wear aswell.
I just did my gears and shift forks. Just do it with the engine upside down so you don't need to take any of the top end apart
Yes, you split these upside down. That's the way it's supposed to be done. You don't lift the top off with the engine right side up. In fact, one of my next little "projects" is going to be a revolving engine stand so that I can flip a motor and take the bottom off.