I never rebuilt an engine before my rebuild in 09. It isn't really that difficult, plus, yours runs. Mine had a busted grunion, and the rod jammed the piston up into the head. I rebuilt it to 680cc chopped it and it's a blast!
There isn't much to these engines. They are roller bearing ( no babbit bearings) low oil pressure, a great forum to reference. Parts to get up and running are cheap, and when you can afford a true Yamaha piece instead of a cheap knockoff,
You just replace it. The rebuild kit for the top end can be had relatively cheap. I baught a piston kit from mikesxs.com for 550$. I took the kit to a shop, they checked out the parts, and for $45, they skimmed the head, lapped the valves, and made sure ring gap was good.
You can do it with simple
Tools. The most technical part was using a torque wrench. Shoot.....I installed my Pistons in the bore while
Watching tv in bed!!
The most aggregating part was when i ripped my base gasket sliding it down the studs, then waited a week for a new one.