Diagnostic Aids
WARNING: This page is about a different car, the 2008 Chevrolet Cobalt. However, it is still accessible from the selected car via links, so may be relevant.
All manual transaxles have gear play that might cause a clunk. If the transaxle is suspected of causing the clunk, compare it with a similar vehicle. An internal clunk in the transaxle is usually caused by wear between 2 components, or from improper assembly, which would also cause other symptoms.