Diagnostic Aids
WARNING: This page is about a different car, the 2008 Pontiac G5 and 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 two components, or from improper assembly, which would also cause other symptoms.