Originally Posted by m5james

A 2001 5Spd could be a stick or auto. You should consider filling out your signature area w/ some details of your X for future use so people will know better which engine, trans, etc that you have.

As for the clunking, I'd look around at either the guibo or center support bearing, both which hold the driveline from slapping around inside the tranny tunnel. Sounds like a good visual inspection w/ the vehicle on a lift while someone else is shifting the tranny will be your best bet.