Remove the crank pinion gear, the clutch, kick starter, kick pinion, shift shaft, shifter pawl (everything from the right hand side) - remove the case bolts from the LH side - you want the crank and all the tranny parts to stay in the LH side.
Use a dead blow polycast hammer to drive on the RH end of the crank and tranny shafts to get the cases to break their seal. If you "whack" more than 4 or 5 times on each shaft and don't get the cases to break their seal, heat the cases with a propane torch (or put the engine in an oven) and heat to about 250 degrees, then try again. If still no go, buy (or fashion) a tool to pull the case while pressing on the end of the crank. You might be able to go to the local Honda shop and get them to let you watch while they separate an engine. Hondas are usually pretty easy - Yamahas require using a press.
Bore to .020 over whatever it is now. Piston is your choice. I like Numura, OEM, Athena and ProX for simple rebuilds. Wiseco, J&E, Wossner and others are for high perf only. Don't waste money on a high dollar piston unless you are going to push the motor to beyond it's normal limit. Stock compression, stock crank and stock cam chain (unless you are building for high performance). If you are building for hi-perf, don't stop with just a crank and piston - have the valves done, install Beryllium valve seats, install a hi-lift cam and new rocker arms. Dont forget to modify the intake and exhaust. Install a 1 or 2mm larger venturi carb and if you are going all out and want to win, have the transmission gears lightened, install a racing clutch basket, racing clutch, remove the electric starter and starter clutch. When you are done with the motor, start working on the chassis. To take advantage of the extra power the motor is making, you will need to install a racing rear axle carrier and eventually make other changes to improve handling and control.