My guess is that you got universal joint problems at the rear end half shafts. One or more universal joints have too much slop in them and causing the clunking noise. Of course could also be the universal joint going into the differential; same problem just different location. I have a 6speed too but no problem at this point. I have experienced this clunking noise problems with 1 or 2 Corvettes and this rear-end drive is very similar.
Let's see how close I am to diagnosing this problem. Let us know specifically what the problem is.