Did you make this repair or get any help? It has been a couple of years since I have split a YTM case but I have been through a few. The worst part is stripping case bolts; make sure you is a good hand impact on those Phillips bolts. I would have a shop manual with me though.
Have you pulled off the clutches to inspect the shift mechanism? That is more often the problem. That is where I would start. I have bent one of the internal sift fork shafts before, that was the first time I had to spit a case.
1984 Yamaha YT 60 Tri Zinger(current project)
1983 Yamaha YTM 200 (rear suspension kit)..... long term project
2004 BMW R1150R
1972 Honda CT 70
2007 Lifan 110