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1999-2003 will work as a direct bolt in. Those should be all PI (Performance Improved) engines. 97-98 were not PI and most 04-up are 3V engines and are a totally different animal.
Also 04 Superduty 5.4L are the same as the 99-03 F150, but have different intake and exhaust manifolds I believe.
I assume that 04 and up 3-valves have everything changed. Computer, Emissions, Gauges, Wiring, Ect... Could be done but not worth the effort of 6 months of hacking and splicing together.