I went through the same issue with our LX a few years ago. Check the area where the harness crosses over from the body to tailgate...it's a section that flexes 90 degrees every time you open and shut the tailgate. My past life included designing wire harnesses for various flying machine, and normally you find a much longer flexing length than Toyota did...i.e., they blew the design. My fix was to remove the plastic piece that drops down with the harness, or it will drive you crazy.

You'll need to remove the harness outer jacket with a seam ripper or similar...do NOT use a knife. Inspect the wires underneath and I'll bet you see exposed conductors that are causing your problem. I replaced the bad wiring, insulating with heat-shrink. I also used heat-shrink to recover the outer insulation on the harness. No issues after that. ETA...you' will need to get more of the harness out of the tailgate to make the repair, meaning remove the carpet pad from the tailgate, remove both left and right internal covers and release any wire holders so you can get 4-6 inches of cable inside the tailgate outside so you can make the fix. PM me if you need more info.

You could also check Toyota dealers as wiring is identical to the same year Land Cruiser...the price you were quoted is what I'd expect...after all, it's Lexus and you're not exactly in the cheapest labor area in the country. If you'd like a great indy shop with a couple of Cruiser-heads, call A+ Imports. They're in San Carlos about 3-4 minutes from 101. Good folks with whom I've had great service.

hth

Steve