You've gone this far, go ahead an take out the transmission and crankshaft. Everything simply lifts out of the lower case half at this point. The transmission parts you really need to look at are the forks and selector cam. The engagement dogs on the gears are the next likely wear points. Pay attention to which way the seals face. Pay attention where the bearing alignment clips go. Those are the half moon shaped clips that keep the bearings aligned to the cases. the bearing behind the clutch is a full circle ring and won't come off accidentally. Also, the stock main bearings have a little pin in the outer race that fits in a notch where the cases mate. This keeps the race from potentially spinning, but I have seen more than a few get assembled with the pin unnoticed which damages the case. put some grease on the seal lips and mating shafting before assembly. Leave the outside of the seals dry where they meet the case. Use yamabond or three bond or equivalent to seal the case halves. I use red locktite or bearing mount on the main bearings. Assembly should be easy. Dry fit the case halves together without any parts inside. Then dry fit again with the assembly complete just to check. The case halves should come COMPLETELY together easily by hand - no bolts. If they don't, figure out why. If you have not rebuilt the crank, you can put the nuts on the bottom and snug them down to make sure the crank spins absolutely freely. (leave the seals out). If it does not, get the crank trued. Once you are happy that everything is all right, put a thin even coat of sealant on the lower case half and bolt together. Snug all the nuts and bolts down by hand and use a torque wrench to finish. I forget the values, but they are very low. I use blue locktite on mine, but a lot of people don't. I think it helps keep out corrosion, but opinions vary. Good luck!
