Hows that tiny lil spring on the end. Is it bent any? Is the shaft its self bent any? If the shaft is bent even slightly, it will not shift properly and be all out wack. Same goes for the lil spring also.
If that lil spring is bent or broken any way, you have to buy a whole new shift shaft as you cant buy that lil spring separately.
Sounds like you got it worked out though, so go ride it and let me know if its better.
If its not, just grab a brand new shift shaft form Jeff at F.A.S.T as there not that expensive to get.
Later