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Under hood on drivers side between brake resireservoir and fuse box there is 4 spare wires coming from a wire harness; which one/color is best for truck cap light?
Not sure if you're talking about the interior light or the third brake light. For the interior light I just tapped into the 12v positive wire on the back side of the trailer plug at the rear bumper and for the third brake light there is a light green wire ran to the rear of the truck just for that purpose. I ran those wires along with a ground wire to a trailer connector that I mounted in my bed for my truck cap.
Sounds like OP is talking about the 4 customer access wires or upfitter switch wires.
None of those are powered unless you make a connection on either end, they are simply extras that Ford saw fit to provide to make it easier to add accessories.
For powering the cap, refer to the answer above. I am also of the opinion that is the easiest way to do it.