You don't have body mounts, a WJ is a unibody.
The reason I asked about thumping was because the shocks can rattle around over the smallest of bumps. The bushings are not loaded except the fronts at the top.

Ok that eliminates having to look for them.. Thanks..

Yeah the shocks are like 2 weeks old. Everything else that I did is about a month old..

If you just did your shocks did the noise change at all ...this sounds like the bar pins that attach the bottom eye of the shock to the axle or the bushing cups on the top of the shocks