Originally Posted by Water Dog
The second possibility is a bad transmission mount itself. You can check that by using a small pry bar between the back of the transfer case skid and transfer case and trying to raise the transfer case off the skid. If you can, replace the mount.
I have the same problem as OP. I pretty much get clunks shifting through all gears unless I am very gentle with the clutch and match the engine RPMs to the tranny's input shaft almost perfectly, especially when downshifting. I also experience clunks when I am idling in 1st and I hit the gas fairly quickly (usually when driving over speed bumps and such) and I am not even touching the clutch pedal.
I doubt it's the u-joints because I just had the rear u-joints replaced last summer, and I don't think it could be the front u-joints if I am in 2H. When you are using the pry bar, how much should the TC move in order for the mount to be considered bad? I went out this morning and it seemed like I could raise the TC a little bit, but it took a lot of work so I wasn't sure if that was just the weight of the TC or if I was "forcing" it to raise by using so much force.
Edit: also how would I know if the control arm bushings are bad like the OP's?