Well, I did some hacking on this problem. It looks to me like the way it work is this. Ignoring the dash switch for a now, the tailgate just requires 12V to come in. The 12V goes to the key switch on the gate and depending on the way the key is turned, routes the 12V either to the blue or pink wire (12V is orange). The motor has a connector with two conductors, the pink and blue, and one of them goes to 12V (relative to ground, not the other) depending how the key is turned. So, bottom line is that I think the motor must get its ground through the metal of the tailgate, not a through a wire.
I ripped everything open and with the tailgate flat, the window was happy to open but had a heck of a time closing. I disconnected the drive cable from the motor and it spins like crazy either way. I then reconnected it and disconnected the other end of the drive cable and it still spins easily either way. With it disconnected from the motor, I can verify with a pair of pliers that it's easy to turn in one direction and not the other. Something in the gearing is causing a lot of resistance, especially going down.
I pulled the little tracks off that attach to the bottom of the glass and they were pretty grungy. I scrubbed them out and lubed them lightly, but this didn't make much difference. I also pulled the little assembly that converts the drive cable to gearing, but I wasn't really able to get it all the way out. It was disconnected from the rest of the assembly though, and I could tell the motor was happy to spin this much either direction. So, the bind is someplace in the big gears and arms.
Generally, there is a lot of sandy grit floating all over the place in the gate. I'm not exactly sure why, but maybe it's byproducts of my recent body work and paint job that found their way in there. It's working a little bit better since I was pulling stuff apart and oiling around, but it's still pretty slow. I'm considering opening up the access panel and pressure washing in there to blast out the grit and stuff. I'm not sure if this is a good idea since it might de-lube everything and the grit maybe be embedded in grease anyway.
These things are kind of a PITA. If it was easy, I'd consider switching to a manual rear window instead.