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You say it will not go down, but when you have it down via the jumper, will it go up via the switch? Also note the driver switch must be in the center position in order for the tailgate switch to work.
You are correct about the switch. It is in the left hand latch. Close the gate and press on the left side when you are trying to operate the window. If it works you need to adjust the position of the stud that the latch locks on to. You can also pull the connector at the switch and jumper it out to see if the window will work, but you have to have the gate down and window in the up position to get at it.
A lot of people have bypassed that switch and assume the responsibility of making sure the tailgate is fuly closed before operating the window. The advantage to that is that you can operate the window for maintenance when the gate is down. If you do that, then you need to support the window when it is in the up position and make sure it is retracted before shutting the tailgate. In other words you become the safety switch.
There are other possibilities but try this first and let us know the result.
Here is the electrical diagram for the tailgate motor,
http://broncozone.com/topic/15889-tailgate-wiring-diagram/?hl=tailgate Also go the the HowTo section of the forum and search on tailgate, you will get several hits, this being one of them.