Instrument cluster, fuel system, PATS, etc.
Your 94 Explorer instrument cluster has an analog interface to the PCM. I suspect the 2005 Mustang instrument cluster has a digital interface to the PCM.
Your 94 Explorer has a return type fuel system with a fuel pressure regulator on the fuel rail. I suspect the 2005 Mustang has a returnless fuel system with an intank fuel pressure regulator, a rail mounted fuel pressure sensor, and a fuel pump driver module that interfaces with the PCM and the fuel pump.
I suspect the 2005 Mustang has PATS while your 94 Explorer does not.
The Mustang may have drive by wire throttle control while the Explorer doesn't.
Without giving the swap a lot of thought, I think the easiest configuration to implement would be to use a 1997 Explorer PCM (return type fuel system and no PATS) and a 1997 engine wiring harness. You'd probably need to replace the Mustang thermostat housing with an earlier Explorer housing since I think the Mustang housing only has one ECT sensor. The 1997 SOHC V6 has a variable intake system and differs significantly from the 2005 Mustang. Aren't the air filters on opposite sides?
In this area a 1st generation Explorer with a blown engine or transmission sells for about scrap metal price ($500 to $800). A 2nd generation Explorer with a blown engine or transmission sells for about $800 to $1200. I suspect it would be less expensive and more likely to complete to buy a 2nd generation with a blown or timing chain failed engine and then use the Mustang long block. Everything else could be sold for scrap metal or parts. The only advantage of using your Mustang engine vs just buying a functional 2nd generation Explorer are the timing chain improvements and lower mileage.
