I've had a few clunking issues. All solved.
-Wheels, goodyear didn't tighten the lug nuts properly, It made a noticeable clunking sound on release of the brake, etc.
-Slip yoke, needed to be greased.
-Leaf spring bushings, the metal sleeve was wallowed out, so I replaced them. (The whole leafs.)
-Loose u bolts, groaned and clunked.
2001 XJ, patriot blue, 4 inch RE lift, IRO long arms, 33's. Caged, locked, armored -Trail Rig
2004 WJ Special Edition, Silver, 3 inch IRO lift, 4.7, JK graphite moab wheels/SRA's- Mom's dd
2004 WJ Overland, Onyx Green, 90% dechromed, soon to have JK moab's, BFG MT's, and a 3 inch IRO lift My new DD/ project