If I'm reading this right the OP is referring to the bucking bar (pin in center of the sprocket) that is protruding further than it should. If I'm right it could be that the ball bearing is binding or the bar itself. They should both slide in easily until the bar is protruding just a little more than 1/4", maybe 3/8". If not, sumpin' is wrong. That pin (bucking bar) is only a little over 1 inch long. If it is protruding 3/4" there's a problem.
Did you do any adjustments to the right side of the clutch components? The flower nut, pressure plate or did you hammer on the clutch cross shaft in either direction?
As Maniac said, the bucking bar, ball bearing and the cam in the clutch actuator cover should all be well lubricated with grease prior to assembly.
Is the clutch actuator arm pointing toward the rear of the bike when you try to install the cover? It should be.
Tom