Ok to update on my experience with this I finally replaced the last parts that I had yet to replace. I replaced all the ball-joints and I swapped out my JKS lower control arms for some rebuilt RC ones I had lying around that I was just going to give to my buddy as a gift but I wanted to try them out for process of elimination. After my initial test drive I drove around and hit areas that usually made the clunk sound and I couldn't hear anything! I am very pleased! I am about 95% positive it was the ball-joints since the lowers on both sides seemed to be pretty worn out even though there was no noticeable play in the knuckle. The nut for the lower driver side ball-joint was completely loose to the point where I didn't even need a wrench to get it off, it just wiggled back and forth on the cotter pin which if it wasn't there the nut would most definitely have fallen off. The uppers still seemed to be ok but I got my ball-joints from alljeep.com and they have a killer deal on set of upper and lower ball-joints so I figured with 210,000 miles on the originals it couldn't hurt to go ahead and replace all of them.
So after all this I replaced the track bar, all control arms, sway bar bushing, sway bar disconnect bushings, motor mounts, transmission mount, and ball-joints. But like I said I think it was the ball-joints that did it.
