[CrustyNoodle]

I can't offer any solutions but I'm very interested to hear what you find. I also have a Wavetrac and "the thump". I'm not entirely sure it is the Wavetrac but I have my suspicions.
If you can afford the time, you could put the old diff back in and see if the clunk disappears - that would definitely indicate that the issue is inside the diff not outside (driveshafts or bushes etc.)