Dan -
Lots of pics, lot of detail, complex area. It is like looking at a knitted sweater, one stitch at a time, and trying to determine what each stitch is doing as part of the whole thing.
Big picture? I think that if we are going to unscramble the situation for you, you are going to have to create a sketch of what is connected to what. You don't have to draw the physical placement of the wires, or their physical routing from one place to another. But the sketch does need to show all the wires, all the electrical connections between the wires, all the dead ends where a wire is not connected to anything, and all the devices (fuses, switches, etc) that are part of the whole. It helps if you indicate the color of each wire in your sketch.
Making the sketch is not hard, but it is painstaking. We have a number of electrical experts on the Forum who can decipher your sketch and tell you how everything works. Help us out here, so we can help you.
Bill
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