I would just move all the wiring over and get rid of anything you don't need. On my sunfire swap, the window, lock, and remote entry wires all get taken out along with a few others. The electric seat wires can go too. That will take a lot of wires out of the harness and will get rid of a few module boxes.
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1991 F-250:
4.9L, Mazda 5 speed, 4.10 10.25" rear
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