2 of the little pins in end of shift drum were in wrong places...fixed that
Hmm, tell us more about this part? It's pretty hard to get those pins into the wrong places, one is shorter than the others and the holes in the plates should dictate what goes where.
Got pics?
When you TRY to shift up into third, what actually happens? Can you not lift the lever, or does it go up but leave you in 2nd, or does it go up and leave you in a false neutral?
Take the shifter cover off, put the shift lever back onto the shift shaft, and then operate the mechanism as you roll the back tire. Watch the shift pawl arm, see how it ratchets over the pins as you lift and then release the lever. When you reach the upshift to third, what happens?
If the shift mechanism is doing it's job, then you have an internal problem and need to split the cases again. Perhaps you missed getting the center fork aligned with the secondary shaft gear when putting hte cases back together?
mystic_1