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Pull the panel off of your tailgate and find the harness clip that connects to you window motor. Try to hotwire the leads on the connector to move the window. If you get nothing then you definately have a motor problem. If this is the case you can disable the lock that prevents you from opening the tailgate. I cannot recall exactly how I did it, but it was as simple as locking out a spring loaded switch which is also behind the panel. Anyway, this would let you open the gate to get your box and work on the tailgate.
There is a bar that attaches to the release for the tailgate and runs to the bottom of the tailgate with a small "L" Bend at the bottom. The window hits this and when pushed down, allows the tailgate to be opened. You can pull this down when you remove the panel and then open the tailgate. Make sure you have someone else there to catch the tailgate in case it drops. You will also want something to prop the glass a bit while the tailgate is down or you will shatter it.
It magically started working again, something is obviously loose. I ll pull everything aprt this weekend. I just hate to pull the carpeting off the tailgate.
If the window is intermittent depending on conditions...I would check your connections. Check all the plugs in the tailgate...I'm willing to bet that the same connection on your truck is the same one as in my truck that was ****e. Try cleaning all of your connections with electrical contact cleaner and a toothbrush...then dab a fair amount of dielectric grease in the contacts before plugging them back together. The plug that was bad on my truck was the direct plug to the motor.
Don't forget the plug that is just inside the drivers side fender. Just pull the boot and there it is. Also check your wiring harness from the tailgate to the fender. I had a broken wire that would make contact once in awhile.
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