I have a 2000 excursion with a 5.4 and just bought a 2006 expedition with a 5.4. Can the 06 5.4 be swapped to my excursion?

 

Anything is possible, but that's a very involved swap. Your 2000 has a 2 valve engine and a 4R100 transmission with medium duty emissions. The 2006 has a 3 valve engine with a 4R75 transmission and light duty emissions. There are a lot of wiring and electronic differences and that swap just wouldn't be worth the hassles. The Excursion PCM won't run the 3 valve, and the Expy PCM won't run the 4R100.