So I swap a 95 12valve into my 03 6.0 Powerstroke with an automatic originally. I used the 47rh transmission so now what’s left of the ford computer doesn’t see any gear position from the transmission, this results in the truck not starting with the key and no 4 wheel low. What’s the best way to fix this?

The truck runs and drives great, almost everything else works great electrically, I think I split the intercooler running 100 psi of boost through it tho. The other issue is the coolant temp started acting up and turning off and on/working intermittently, it was running fine after the conversion so I think it’s a ford equipment error not resulting from the conversion