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dcsmith, I sent you a PM, but I'll repeat it here for everyone else's benefit. The controller doesn't need to be connected to anything other than the wires that it has. I don't know about the 92-96 trucks, but the later models I have worked on have five wires on the truck harness, while both brake controllers I've used have only four wires.
The controller's four wires have the following functions: Power, Ground, Brake light signal, and Brake control output to the trailer. The truck harnesses I am familiar with have: Power, Ground, Brake light signal, Control output, and Backlight. Backlight just supplies the controller with a signal from the dash lights, should the controller have a display. If the controller doesn't use the backlight, just tape that wire out of the way on the truck side.
As for matching up the wires, match function to function, NOT color to color. Per the colors that dcsmith posted above, brake controller white goes to truck white, blue to blue, controller black to truck red "feed wire from battery", and controller red to truck green "stop lamp". Illumination feed is unused by this brake controller, so tape the end of the unused wire.
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