I'm not too familiar with XJ setups and no searches seem to give me a theory. My XJ 4x4 5spd makes a clunk noise if I hit a bump hard enough. Typically it's just a single 'clunk' but enough force can get a chatter out of it. Just riding over bumps or riding slow on the rough residental roads typical of Duluth, MN won't cause any noise.
I've replaced all four shocks, I looked underneath at the trans and transfer case and nothing seemed broken. The axles checked out ok too. It has 185k on it. So far no adverse results of the noise just annoying and worrysome.

Check your exhaust system and the control arm bushings.

I was under my 99 yesterday. I realized my tailpipe was hitting the axle where it goes over it. Check there.

Exhaust is where I'd start.

Alright, I'll check out the exhaust. Could a worn track bar cause it?

Track bar could, sure. Anything with rubber bushings, really.

I replaced what I thought was everything under my front end that would be causing this same noise, shocks, sway bar connectors, TRE's. Finally at the shop that was mounting my new tires I asked them to take a look at my CA's as I thought maybe they were causing the metal on metal noise I heard every time I hit a bump.

Turns out my CA's were in great shape, but they guy who looked at my truck said it was probably my sway bar to frame bushing that were the culprit as they looked pretty worn.

I went home and put new ones on and boom. No more bang when I hit bumps.

Ill still check the exhaust system, but the sound seems to be on the drivers side and up front. My sway bar bushings on the frame were shot and causing a clunk but I've fixed that issue already.

Are you sure it isn't your transfer case linkage? The brass grommet wears out allowing the torque shaft to bang around inside the body mount. May want to check that as well. You can get a rebuild kit online for it for about $13.

I looked at the linkage bushing and it is pretty well worn out, I held up on the transfer case shifter while going over bumps but it would still make the thunk.

I noticed now too that a clunk occurs when I shift from reverse to 1st (and vise versa) and begin to move. I crawled underneath and found I can push the transmission up and move it some. I assume the mount must be worn out and sagging. Do the autos and manuals share the same tranny mount?

Depends on the year - apparently NV3500 XJs don't, but IIRC 1999 does. If you look up the mounts on NAPA or RockAuto.com and compare part numbers that will tell gou.

I'm leaning as this being the cause. The clunk sound seems to match the shifter bouncing as well. taking off in 1st I can see the shifter move as if the torque is lifting the trans off the worn out tranny mount.

Sounds similar to my old motor mount problem!
Might as well take a look at yours and make sure they are good.

its generally a good idea to replace the motor mounts when you do the tranny mounts. doesnt take long to do, all three (2 engine 1 tran) probably took me about an hour and a half by myself. the rubber in my stock mounts were in 3 pieces. just do em one at a time in one sitting though, dont take one and then the other, take off-replace reinstall. take off, replace, reinstall. good luck!