I talked with my cousin agin, he's the one that was looking for a med. duty truck w/T444E last spring and I learned a lot about the programming possibilities from him.
He said the Allison auto trans has NO wires going to it, so in the end I don't see why you couldn't just use a Ford PCM if it'll bolt up to the IH harness and run the truck, it should work. Or at the very least, consult with a chip programmer (Tony Wildman or DP Tuner) with the PCM code on the IH motor and see if they can tune for it straight up. These guys are always finding new tuning things, so you never know.