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The tail gate window is easily to trouble shoot if you can use a volt meter. Diagrams are attached to the bottom of this post. There are a few quick checks:
1. Check the fuses (2)
2.

ush in on the left side of the tail gate while using the tailgate key switch, there is a switch inside the left latch that prevents operating the window when the gate is open, (most people who have a problem with it have it bypassed). If that doesn't work, open the access panel, find the red and yellow wires along the bottom edge of the opening, if the motor connector is easy to get at in your truck, disconnect the motor and jumper it to 12V, reversing the connection reverses the motor direction. If this works you have a wiring or connection problem, (not uncommon for an older vehicle), and here is where a volt meter comes in.
3. Eliminate the left latch as a problem by reaching in by the latch and removing the connector, (kind of a pain to get to), Use a wire to jumper it at the connector and place it out of the way of the window. If that works I'd leave it bypassed and hope your are smart enough to close the gate before closing the window. It is also an advantage to make servicing the window mechanism with the gate down, (just be careful since the window is not supported. I usually place a sawhorse under the window when I have the gate down and the window in the up position for service).
4. Use the voltmeter to determine where the problem is, (if you have gotten this far it is most likely in the ground return path.
Good luck,

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