Need expert help, wont shift past 3rd when right cover gets bolted on

[Brueske]

Like the title says, its shifts good through all gears when the right-hand crankcase cover is off, but when you put the cover back on and tighten all the bolts down it will not shift above 3rd gear. Motor is out by the way. Im only the messenger here, my buddys are the ones working on it. The motor was taken apart and carefully re-assembled also.

[wonderboy]

What motor?