The tranny can be very tempermental if anything is even slightly off. Every little washer and spacer is a different size or width, and they MUST be in the right spot. I don't know how far you disassembled, but you will need to go back over everything you had apart and double and tripple check everythinguntil you find the problem. The first an easiest thing to check is the ratchet mechanism on at the end to the shift shaft. Check that stuff first as it will not require splitting the cases just remove the clutch side case cover, you will probably have to take the clutch out too, something may have just slipped out of position when you were putting it back together. If that is all ok, then you will have to get back inside the crankcase. Make sure the shift forks are in the right spots. Check to see if all the gears are lined up properly, turn them around and make sure they don't catch or stop, they should turn all the way around without interference. I lost track of the washers in my CR 500 motor and had to buy all new ones so I could reference the part #'s and find out where they go using a Honda part fische diagram. That was a real pain. Good luck.