Update...My motor mounts looked a little "squatty" so I thought I would try replacing them, although they only had a little over 40Kish miles on them. I replaced the transmission mount at the same time, as it was showing plenty of wear as well. My old motor mounts were a full 1/4" shorter than the new mounts. Amazing how much wear in 40Kish miles. No change in the clunking though. The UCAs are the only thing I haven't changed. I lifted the Jeep under the LCA on both sides (to keep it at a normal ride height) and hit around the tire with an 8lb sledge hammer while holding on to the UCA. I felt 0 movement/contact/looseness in the UCA. It was tight as can be. The UCA is the only part I haven't replaced, so I may go ahead and try it.
It's current state...no noises while engine/driveline has stress applied to it. I can accelerate and drive down the highway just fine (as long as my foot is slightly in the throttle). Not a peep. As soon as I let off the go pedal, brake, or turn hard (while not accelerating), random clunking. I would describe it as someone randomly tapping/hitting my firewall with my 8lb sledge. Very loud, very noticeable, very annoying.
WWDiesel...the outer bushings on the wishbone on the rear axle were shot on mine. My mechanic had just swapped out a rear end on a Libby and gave me the good used one off of that. I swapped it out on mine. I did notice a difference in handling and ride, but it wasn't my clunking problem either.
I'm taking it to my mechanic's shop on Thursday to give it another look on the rack in his shop. As I've said before, he is a former Jeep dealership mechanic and is very familiar with the most of the issues the Libbys had. His is just as stumped as I at the moment, and has been very helpful as he wants to find the culprit for his own knowledge. I'll post an update next week. In the meantime...alcohol will help.
Late update...I just took it for a test drive down the highway. Clunking like heck going in a straight line on smooth highway pavement (minimal-suspension movement). I'll post next week what I come up with.