Has it seated properly on the dowel on the hole, at the front end (lower)?
It should go on flush, or something is stopping it. Check the dowels, then for any external obstructions.
Warning, do not go pulling this cover about or you are in danger of the kickstart mechanism coming out - and believe me, you don't want that to happen.
Look on the inside of the cover - if you see any scratches opposite the clutch assembly, look to retorque the clutch bolts to spec (6-7lbs I think).
If that is all done, have a look to make sure the shifter-shaft has not been disturbed and has come off its spring - if so, replace.
tshadow6, leave that mallet where it is - gently and patiently does it.
Anlaf