1. there is supposed to be a half moon cut into your shift shaft. It is so the bolt will go through without fouling.
2. Is the spline worn off the shift shaft or the shifter? Make sure you know which is worn.
3. To remove the shift shaft(if nessacary) Drain oil, Remove clutch cover, Remove clutch and basket, remove shifter(if you havent done so already), pull the shift shaft right outa there.