My boat (the one rewired with zip cord) has two trim tab switches, one on the flybridge and one at the lower station. Could your extra set of wires be for the other station?
When I redid mine, I ran new power and return wires from the trim tab power switch on the eyebrow panel, and ran new wire from each trim tab control switch back to the terminal block on the trim tab pump. This way, the two switch circuits are redundant (always thinking damage control in case I get in a shootout) and it was actually easier to run the two sets of wires independently rather than try to double them up on the lower control switch, or put a terminal block in the middle somewhere.
I could not find 6-wire cable with the right colors, so I made my own up with white wire and put colored shrink tubing at the ends. Soldered eyes. All of the problems I had been having with the "old" unit disappeared with the old wire.
1975 32' Flybridge Sedan, twin Perkins 6-354 diesels, 1:1.53 velvetdrives, 16 X 19 props. Merritt Island, Florida