id look at that small gear that came off, i just rebuilt my tranny, i believe there is a washer that goes on the end of that shaft. it goes gear then washer. you may have the washer on the inside of the gear. You said you replaced the bearings, are they in all the way to where they seat. one of the cylindrical roller bearings may not be in all the way. Id take a closer look at all the diagrams and what you have.
Make Sure everything is clean clean clean. And i def. recomend using yamabond to seal the case back up. That stuff is by far the best gasket maker there is. period. Its a semi drying liquid gasket. Hands down the only stuff ill ever use. the book recomends it for sealing up the case halves too since there is no gasket.
1985 Yamaha Tri Z 260PV
Suzuki Trail Buddy 50