It's not so much the engine, it's the drive by wire, pcm, and harness. Ford has changed that for the mustang guys, the 3V 4.6L is a drive by wire twin throttle body, so Ford racing has released a throttle body that is used by throttle cable, and tps for the swap for those vehicles that don't have drive by wire. So now one can retain their pcm, and mate up the engine harness, and get a custom tune done, go on their way.
So i am sure something can be done in this situation aswell.
2008 Oxford White F150 FX2 SPORT Super Crew,5.4L.
2003 Satin Silver Clearcoat Mustang GT,4.6L 2V,5 speed.