Hello, In all likelyhood the clunk is the dread "double bump" which is part of the 2001 5 speed experience. I have it in my 2002. The transmission download helped as did 2 transmission sump drain and fills. A complete flush (not a power flush via some machine)of transmission fluid might soften the bump a tiny bit but the clunk you feel is caused by the valve body. You should get your claim in first thing in the morning. That would be Monday December 6th, 2010. Said bump will be more pronounced when the fluid is warmed up. There is a valve body rebuild kit from Transgo(California) and I've found a guy near me who'll rebuild one for ~$3,500. A new transmission installed at a dealer will be ~$5,000.
They know the transmission is a stiff. The entire automobile industry knows it's a stiff. I think the best thing to do would be to get them to take the car back and pick something else-even from them. How much did you pay? Roughly where do you live? Kira