Could the thumping be universals? I've got a similar problem except mine is fairly consistent when shifting into reverse which is usually a sign of universal joints going bad.

I put the truck in the dealer today. The guy looked at me like I had 2 heads when I described what was going on. I got the impression that he is going to try and sell me on a trans but I ain't goin for it. None of this started until I changed the fluids. So they're doing a trans flush for $180. Service both diffs for $300. Not sure what they do for $300. And service the transfer case for $160. which has never been done yet. They're also gonna road test it and check out the thumping for another $90. I hope all this fixes something at least? I'll post the results ASAP. Thanks guys. Bill