Usually when it's reduced engine power it's an issue with the APP sensor or the throttle body. If it happens with bumps then could be a possible wiring/terminal issue, however I haven't dealt with Jeep's.
I have a buddy thats got a lmm doing the same thing right now. Towing 16k with a straight pipe, air intake and 120hp hp tuners tune (they go by flywheel hp) its reducing engine power and won't go over like 1800 rpms. He said autozone said there was no codes. Its fine without the trailer so im guessing the transmission isn't happy with the load to power ratio? Anybody else have this problem?