the only thing that may give you trouble as i understand it is the transmission as most 4.6's were running a 4r70/75's and 5.4's 4r100's. the TCM requires different wiring and connections, and the TCM for the 4.6/4r70/75 isn't capable of producing the voltage required to operate the 4r100.......... so..... the PCM can likely be flashed but the TCM will require one intended for a 4r100 (if in fact that is what is behind that particular engine/build) as well as it being flashed for the pressures of a Expedition (torque management; valve body/solenoid pressures)... otherwise, you're in for a choppy ride.
what year are you talking about?
if you're dropping a 2v 5.4 in the place of a dohc engine, the PCM will have to be swapped- likely true with any of the variations from 4.6/5.4 2v/3v/4v and sohc/dohc.... so.. bank on a PCM flash/swap at a minimum, and a PCM+TCM possibly/likely.
Romeo and Windsor engines are different, too- not that it should impact for a simple (simple?) swap, but.... be aware of that, as well.