Complete Bike Rebuild?? Worth it?

Got the engine off boyos
 

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Top engine (valve cover) off. Done for the day, i need to do some research on the timing chain and valves, if anyone has some guidance that will make reassembly easier. Also, @Bushyeyed1 do you know what this etching is, it says shell?
 

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Sorry it’s been so long folks. I have been doing a bit of work here and there, but it’s slow going ive been reading clymers as i tear it down and I’m pretty bad about using pc’s. I have the entire top end torn down, and am almost done cleaning the parts and working on my list of parts for ordering.

I notice a lot of carbon buildup on my right side piston that isn’t present on the left side. Im not sure if this is somehow from the loss of compression or if there’s another issue i have to chase, hopefully something simple like air/fuel mixture problems (my guess) or spark plug issues.

I’ve been consistently working on it, but man, i’m absolutely ignorant when it comes to engines and i’m trying to do it right with clearances. I believe that with the engine being bored out the piston/wall clearance will be different than clymers recommends and i’ll have to research that, but would this affect clearances elsewhere?
 

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Good progress!
RH piston top looks like oil burning to me.
Ok so if I’m starting to understand this correctly, the piston rings could be bad on that one, leading to a poor seal that allows too much oil to get up there?

Wont matter if thats the case because i’ll be replacing both pistons (getting the cylinder honed today so i’ll know what size to get)

@gggGary i really appreciate how knowledgeable and freely sharing all you are. I’ve been reading through the clymers manual and starting to read through the tech forums so i am starting to get some idea of how an engine works but troubleshooting is still a struggle.

I am still of the mindset i at least want to tear everything apart and measure clearances and put it back together for knowledge, but would you recommend i just fix what i know is broken so i can get the bike back on the road?
 
replacing both pistons (getting the cylinder honed today so i’ll know what size to get)
Wrong order. You buy pistons, then have a machine shop bore/hone the cylinders to the correct diameter. Before you do that, clean everything up and give is some pics of the pistons and liners. There's a chance you can go back stock with new rings.
 
Wrong order. You buy pistons, then have a machine shop bore/hone the cylinders to the correct diameter. Before you do that, clean everything up and give is some pics of the pistons and liners. There's a chance you can go back stock with new rings.

Maybe still Possible Go stock with a new stock piston Perhaps not easy to find one especially if needs to be paired with the cylinder class.
Depends on plans and wear
 
Maybe still Possible Go stock with a new stock piston Perhaps not easy to find one especially if needs to be paired with the cylinder class.
Depends on plans and wear
The problem is that it’s not stock right now, its bored up to 702, so i cant go stock pistons
 
Alright boyos, bad news, the left cylinder (the piston that got punched out) is .004” and the right (with all the carbon buildup) is a whopping .006” and out of round

With this im thinking the easiest thing to do would remove the sleeves that are currently in and replace them along with new pistons. Thoughts?

If i do this my plan is to remove the liners myself and take it back to the machinist to have the liner/piston matched and the liner surfaced to the head height (think i said that part right)
 
So after some thought, i think ill buy this stock kit from mikes, the current cylinders already bored out to 78mm for 706cc so its looking like unless i go up to the 750cc big bore kit (which requires a LOT more machining on the engine, and im an inexperienced rider so loss of power won’t be noticed i didnt use it anyway) the cylinder walls may fail (if im wrong please feel free to correct but i cannot find 78.5-79mm pistons).


https://www.mikesxs.net/yamaha-xs650-650cc-replacement-cylinder-and-piston-kit.html

My thoughts are, by buying the kit i shouldn’t need the cylinders honed (right?) so it should be 560 to drop it in and run. If i were to use the current block, itll cost me about 250 for the new sleeves (jugs?) plus 120 to get them honed (300 if they need to be bored at all) and 220 if it needs to be surfaced, plus pistons, so its roughly the same or a bit less for way less work.
 
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