I would do a compression test with the engine warm before I tore the bike down. If you have to rebuild the top end, make sure you don't put the new piston in backwards. The gap on the piston ring goes on the carb side. Also make sure to use the new piston pin clips. The opening on the clip should be either up or down. If it faces toward the front or rear of the piston it has more probability of popping out from the force of the piston going up and down. I like to coat the rings and skirts with engine assembly grease before I put the cylinder on. When you are bolting the engine in the frame, you will have an engine mount on the head. Make sure you torque the head before putting this mount on. When you put the head to frame mount on, tighten it to the head first and the frame last. I also mix my first tank with petroleum oil for a faster break in.
When yuo pull the cylinder off, have a machine shop check the bore for taper and round. If you have to send the cylinder to a chrome shop to be re-nicked, let them know what clearance you want, probably .0020, but that is just a guess, I'm sure someone on the site can give you a more educated measurement than I can. Also, never send the wrist pin bearing to the chrome shop, you will never see it again. Good luck.