I do all my own work but then again I worked as a bike mechanic for twelve years.
You do have to remove the motor. The case is in three parts. The lowest section has to be split to get to the tranny.
The oem manuals are normally pretty good. They do however leave out basic info a newbie mechanic might need.
Parts I can rattle off the top of my head you will need.
1. Clutch cover gskt
2. RT side (starter clutch) cover gskt
3. Lt side (magneto) cover gskt
4. Oil Pan gskt
5. oil pump idler gear circlip (2 of them)
6. Counter shaft circlips (aproximately 3 of them)
7. Two gears on counter shaft (2nd and 5th I think)
8. Shift Fork
9. Shift drum
10. Upgraded solid shift fork shaft
11. Yamabond 4 case sealer (my personel preference)
12. Clutch hub nut (suggested replacement but not absolutly necessary)
13. counter shaft seal
14. Clutch push rod seal
15. water pump oring
16. Oil and filter
17. Coolant
I can change out a tranny in about 6 hours but I have done many.