Was the ignition switch turned on during the time that the battery was reversed? The reason I ask, is that a lot more stuff was exposed to reversed polarity if the switch was cycled, than if it wasn't. Kind of sounds like it was, though.
And you're right; by '89 the underhood fuse box replaced fusible links. I'm sorry that I can't help you much here; I have never ran into a battery polarity reversal situation that was anything more than replacing blown fuses, links, or melted wires to get things back to normal. I've seen tons of individual radios, amps, control modules, etc. fried, but this is a different situation, being a battery reversal versus a component mis-wire. I simply don't know with any certainty what all could have been damaged here, in the individual systems and components.
If it helps (I hope it does, anyway), if I had to deal with this, I would get my hands on the Ford EVTM, or any wiring diagrams on that truck, and start checking all of the power circuits from the battery back to each problem component. For example, is each and every fuse actually passing power? Is the ECM getting power like it should? The coil and the ignition module? It's probably going to take a logical and methodical step-by-step tracing of the circuits back from the battery to sort this thing out. Sure was a pisser of an accident, and I wish you the best luck in getting it fixed.