On my '70, the sensor is mounted on the body on the drivers side- it kindof looks like a door striker, but has a little plastic rod that sticks out. I don't know what year yours is, or how different it is, but there should be a sensor to tell whether or not the tailgate is up or down. If it's down/open, then the tailgate window switch won't work. You might try looking in your haynes manual, connecting the wires for power that are hanging out of the hole(they might be the same color/markings)- that might allow the motor to have power. One of them might be a ground though- so you'd have to ground that somewhere. I haven't messed with the sensor- but there are three wires to it? Power in, power out, and ground? I don't have my manual with me- just looked at the sor page.
As far as the wires in the tailgate- so you have the inspection panel removed, the glass is down, and not allowing you to get to anything inside- it's a tease, isn't it! Depending on which wires are left, you might still be able to operate the window. You might try using the key in the tailgate lock, and turning left and right with it. Or try the dash switch again, when you get a little more juice to work with. Here's the ordering page from sor to look at- mainly, it is an exploded view of the tailgate.
http://www.sor.com/sor/cat138.tam?xax=32437&page.ctx=cat138.tam
Yes, you can remove the glass- but the only way I was able to do this, was to have the window fully extended. There are two clamp/holders on the bottom of the glass, that have runners in them- so the arms of the window gears have little wheels that fit in the runners. I did not remove the runners- and with the window all the way up, and the tailgate all the way down (window supported on boxes, like I mentioned eariler) I was able to wiggle the glass from side to side, up and down, and get the glass detatched from the wheels that fit in the runners. I can't remember how the glass is removed from the runners- but it seemed like it was just a tension/friction type fit with rubber gaskets.
As the sticker on the fire extinguisher case reads: "In case of emergency, Break Glass" So if nothing else, you could just break it, and replace it. From what I remember, it is just a piece of flat glass that you could probably buy at a glass shop.... But I guess, only in case of emergency- or when you've looked into replacement options, and come to your wit's end with removal.
Best of luck Cruiser_Guy. If there's anything else I can do, just ask.
Flux core sucks! 
(I think the motor is bad). Is there some kind of emergency crank or ??? The Haynes manual I have talks about a couple of clips which hold the glass but I can hardly see them with the glass down.
and give me the instructions!
