Holy crap I finally got this done. MAN what a pain that was, took like a day and a half.
I ended up running 2 16AWG wires to the rear. One was straight from the positive battery terminal with a heavy duty inline fuse holder right off the battery terminal eyelet, and the other was from AUX1 on my LVJ 6-position overhead panel (these are already fused). I followed the factory harness all the way from the right front corner to the left tail lamp, and also wrapped all the non-factory wiring with braided wire loom, which REALLY sucked to get wrapped in certain areas, especially running over the fuel tank area above the frame.
All of the wiring for the RGB controller, the extra wiring from the RGB strips, the power and ground leads for the RGB controller, and the wires from the magnetic switch are all hidden behind the left tail lamp in the "pocket," which worked great because it's nice and clean looking. I ended up just grounding the RGB controller with a self tapping screw in the tail lamp pocket. The controller is fed by the two power feeds. One is run with the first switch on the LVJ 6-postion overhead panel, which turns the bed lights on whenever the key power is on, and the other is wired to a magnetic switch located inside the left tailgate jamb which feeds the controller power when the tailgate is opened and cuts power when closed. This setup allows the bed lights to be turned on with the tail gate closed by using the overhead switch panel but also to be automatically turned on when the tail gate is opened. Also, the bed lights can be turned off with the tail gate down simply by using the remote for the RGB controller. The RGB controller reverts to the last setting the lights were on even when the power is cut.
The magnetic switch took a lot of measuring, mounting, re-checking clearance, spacing the switches, drilling some small holes for the wires, etc. Once it was all properly mounted though it works perfect. Besides trying to get the wires properly sheathed this was probably one of the most time intensive things to get right. The remote for the RGB controller simply velcros to the left swing case for easy access to it. I can control the RGB strips without pulling the remote off the swing case, or I can take the remote off the case if I'm camping in the bed and still run them.
Overall I'm very happy with how it turned out, even if it was a large pain in the ass. The setup turned out very clean looking and very functional. I now also have a 16AWG fused lead back there to tap into if I have another "small" item that needs powered. The RGB controller/strips have their own inline fuse behind the tail lamp as well.