Have you considered replacing the engine seals, gaskets, clutch plates, clutch springs and big end bearings while it's out of the frame? Generally considered a good insurance idea right now. I know that when ever I pull a motor that I always replace those items. That's when they are easy to replace whether needed or not. Sucks having to pull it all back out in a month because of something else. I swear by Yamabond and Gaskacinch (but that's a shop staple cause of the artwork on the can).

Almost told you to replace the chain but had a notion this was a driveshaft. Now is also the time to check all those cables. I love to replace clutch cables when the bike looks like that.