I would recommend having your crankshaft trued and welded, costs between $50 and $70 and is good insurance. You should also closely inspect your shift forks for wear and damage, now would be the time to replace them. Also closely inspect your bearings for smooth operation. Make sure you do a pancake bearing clutch adjuster to avoid the ball-rod problem again. I prefer the cascade innovations style.
You could look into the rz350 tranny ratios available or some of the billet gear offerings.