Diagnostic Aids
WARNING: This page is about a different car, the 2002 GMC Sierra and 2002 Chevrolet Silverado. However, it is still accessible from the selected car via links, so may be relevant.
All manual transmission have gear play that might cause a clunk. If the transmission is suspected of causing the clunk, compare it with a similar vehicle. An internal clunk in the transmission is usually caused by wear between two components, or from improper assembly, which would also cause other symptoms.