I am getting the clunking sound also . I get it when when I change gears and going from 1st to reverse . The noise in my car is from the pumpkin . Not sure what it is yet . , but if you find out please let me know.
Had that issue with my n/a bird a few years ago. It was the differential mounts. They were not tightened down. So it may be related to the differential busshings as well. That is the first place that I would start looking. Follow that up with the U-joints, tranny and engine mounts. But my guess is that it is dealing directly with the mounting of the differential.
It could also be backlash in the differential itself. If you have high mileage or had had rear end work done (incorrectly) the ring and pinion gear backlash could be out of spec. You can disconnect the driveshaft from the diff and see if you have play in the diff flange by holding the wheels and working the flange back and forth. If you find backlash you are looking at a diff rebuild.
Found out what the clunk was in my car yesterday . When I had my gearbox rebuilt , the mechanic who installed it never tightened up my driveshaft bolts . I also found out that he doesn't work at this shop anymore because he had done this to a few people in the past 3 months . Scary huh?