I picked up my 99 JGCL about 2 weeks ago as is. I have replaced all the brake pads, welded in new inner rocker panels, replace rear main seal (not too bad a job) front pinion seal and an oil change. So far it seems like it's going to be a good truck. I do have some rattling in the rear which I think is the ball joints on the rear track arm. (?) other than that, she is well on the way. I'll have to get some pics posted soon. I think it's a real good looking vehicle, and plenty of power from the 4.0. I have been looking at some lift kits online. I think I have the bug.

 

congrats on the "thing"

 

The rear upper control arm to axle mount ball joint is probably the noise you hear, as you've guessed. As far as I know there's no cure for the Jeep bug, it just gets worse.
And Welcome to CF.