I had the same symptoms on my 500, and unfortunately I had to split the cases to fix it. Without the clutch nut tightened (on a KX500 anyways) the shaft has enough endplay to allow shifting to occur with the shift forks mixed up. When I did the bench test with the bottom end together, it seems A-OK. However, once you put the clutch on, tighten everything up, you only get first and second gear. I hope you didn't make same mistake, because it means going back to square 1. The shift forks were mixed up.