I think for the Cobra heads you need the Cobra wiring harness. There was a guy that put an Expedition 5.4L engine in his GT. It's in the June issue of Muscle Mustangs and Fast Fords.
the 5.4L 2V heads are exactly the same as the 4.6L heads. there is no gain from swapping. as far as Cobra heads, your better off just buying a complete 4V engine.