This sounds like a two-bit answer to your problem but I would strongly suggest you get a factory service manual for your Jeep....and, for your electrical problem, an inexpensive VOM (volt/ohm meter) available at your parts store or Radio Shack.
I just got done resurrecting my power windows and I'd have never been able to fix them without the testing/troubleshooting procedures in the FSM. In may case, none of the windows would work using their corresponding door switches (they would work from the drivers panel). As in my '00 XJ, you probably have a drivers door panel or "module" (as the book says) from which you can operate all the windows, the window lock and the door locks. This drivers door module (DDM) is where all the power and ground circuits for all the other window motors are fed through. I found a loss of continuity and a large voltage drop isolated to the DDM and, with those results, the book said to replace the DDM becuase it is not serviceable. Not really true..... I was able to carefully take apart the module and inside are all the switch contacts. There was a lot of crud built up on many of the switch contacts and after cleaning them all and reassembling the DDM, it was retested with good results. The wiring was reconnected and all windows now operate as they should. There was nothing wrong with any wiring. In the end I figured I saved well over $100 (the cost of a new DDM).
You could blindly replace wires and never fix the problem. Get the book, get the meter and follow the trouble shooting instructions.
Mike
00XJ