I've also got a few things I can't figure out how to remove:
First: This shaft under the clutch side cover is attached to a plate that appeared to only be held in with a single screw. I removed the screw, but no luck with the shaft/plate. I know you normally don't have to remove this part, but there's some metal trapped behind it (looks like a piece of chain or a piece of spring) that I need to get out... also, I'm planning on having my cases vapor honed, so I need them bare. You can catch a little edge of the back of the plate with a hammer and punch, but it's an awkward angle, and I figured I'd better ask around before whipping out the BFH.
This piece is to the left of the shaft in the previous photo. It has a slotted head, and a jam nut on the lower threaded portion. Also it had some of those folding tabs that Yamaha is fond of. I bend the tabs away and attempted to use my cordless impact on the jam nut, thinking I'd have to loosen it, then unscrew the shaft with the slotted head.
I'm not sure if that is the right procedure, that's just what I was guessing by looking at it. But when the jam nut didn't budge, I figured I'd better ask before trying harder.
And last, this is the bearing the shift fork shaft rested in. On the outside of the case, it looks like a freeze plug. Am i right in assuming I'll need to press the bearing out of the side of the case? Then I'll need to replace it with a new one?
Thanks in advance for your help. I wasn't able to find the answers, or clear enough pictures in my Haynes or Clymer manuals.