I agree entirely that the Ford engineers did a great job with the electrical wiring, but I've already made up my mind in deciding to do this; seeing as how I have already ran the wiring from the motor and through the cab. At this point, I'm so frustrated with the tailgate that I would much rather do it this way than squeeze my arms at weird angles to access the wires.
I have had difficulties with t-gate wiring before, A reall PITA, but not as hard as you make it seem. Starting behind the drivers tailight, check to make sure you have no open wires on the bigger wires. If you can move the harness around and make the ohms reading change it's a broken wire or bad connection in between. For testing purposes I've closed the latches with my finger or a screwdriver, if the safety switch is open when the latches are closed and the meter indicates open, change the switch. If there is continuity across that it could be in the key switch at the t-gate.
I found a bad connection between the wiring coming from the body, right behind the connector, body side. I replaced the wire affected, it splices near the bumper as well on my '91. This high resistance through the connection was making the window go up really slow. Remember a switch only has 2 positions, open and closed. If they check open in both positions, change them. If I can find my Haynes manual I'll look for a diagram and see if I can figure out possibles or what you should find when checking the wires with a test light.