Just went out and physically checked the motor and the wires that come from it and did a little research, here is what I found.
There are 4:
One big black one that runs the signal to the stereo. its not directly connected to the motor but is run in the same vicinity and is the same one that gets plugged into the aforementioned photos. This one isn't the problem, as the signal is in fact going to/from the stereo because I do have reception, as spotty as it is. i.e. going under trees and things of the like makes it fades in and out.
The other three that go to the actually go to the motor and are all in a wire harness together. I think are what need to be worked with. There is two silver, one with a red stripe the other with a green one. and a black.
My guess is that the silver wires are the negatives and would be where the power is coming from and the black is the positive which completes the circuit. I answered my own question about the switch, it does need to be three way (up/off/down) on the account of the three wires going directly to/from the motor.
As for your concerns about the bypassing of the head unit. The only wire that needs to actually be plugged into the system directly is the big black one that actually runs the audio signal. in my case, it is currently working and does not need to be messed with. So the problem with power has now arisen. The reception of the antenna has power (covering your concern) but now the issue is how to run power to the switch and ultimately the motor. Would it tap through the blue wire that was mentioned in another post, that supplies power to the stereo head taking away from the power of the sound system or should it be ran/tapped from a wire that comes straight from the battery since everything is run from 12 volts?
