I've had similar problems on my '01 XJ. The power windows and locks were intermittent, and I traced the problem to about six broken wires in the harness between the driver's door and the interior. This is a common problem on XJs, I understand, but I don't know what range of years. The breaks occur in the area protected by the rubber boot between the door and frame. To remove the harness I had to remove the interior door panel, the water barrier (a thin sheet tacked up on the door), and the driver's kick panel. The harness itself wasn't that hard to remove. Once I got the harness on the table and removed the protective cover, 12 broken and corroded wire ends popped up at me. Fortunately everything was color coded and easy to fix.
If you're handy with a VOM (multi-meter) you can check continuity on the wires by removing the interior door panel (disconnecting the connectors at the window switches) and the kick panel where you should find the other end of your harness. Shoot the wires and if any of them are open (no reading on the VOM) you've got a broken wire. Remove the harness and see what you've got.
The power mirrors also go through that same harness, but your other lights and the radio are controlled elsewhere and I can't help you with that.