I don't know if the harness is different, but the '04 has something in the computer system called PATS (passive anti-theft system). Sucks because you can't work around it. The engines are the same however and if you are only swapping mechanical parts it should work. something to note note though, they must be the same trans or this will not work. Easy fix is to use the tranny that's in the truck now. How many miles on the thrown rod engine, mine also threw a rod. Maybe if we find enough people this happened to we can start a class action suit and make ford fix all of our trucks. lol

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'04 3.0 xlt: thrown rod = dead.
Planned mods: 5.0 swap (got the donor already, it's nardly), 4/5 suspension drop(DONE), traction bars, 8.8swap, 3.55's w/LS . Auto to Manual conversion. Lots more in the works.