I'd say you have bad lube in the transmission: drain, pull the trans, and look for damaged forks and slots. If the slots widen and/or the forks narrow, shifting can become increasingly difficult and less accurate.
For God's sake, avoid that old "jungle biker" trick of adding just a tad of molybdenum to your oil to "fill out the rough spots." Use more than just the right amount, and it will lock up on you. The trick is to figure the right amount: until you open the cases and check, you won't have a clue.
The forks should clear the slots by about .003-.004" at most. If it is wider than that, you're into it for a new transmission.
