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I have a 99 Exy with a 5.4 that needs to be replaced, and engines are hit or miss as far as year and mileage over a messed up price scale in the area I'm in. my question is if I find a 3 V or a DOHV from a later year, can I put it in along with the matching wire harness and ECM?
Well, anything is possible, but I'm sure it will not be an easy thing to do.. The original harness for the rest of the stuff in the truck wont fit the new PCM for the new 3V engines as these came from a whole new generation of expeditions, and then all the rest of the stuff wont fit any engine harness for the 3V 5.4.. Of course the transmission has to be upgraded as well, with the 4R75E that the 3V were paired with. Sure, it's probably possible to swap out all the critical sensors and stuff and make it run, but I think the other systems in the truck wont play along that easily, or the instrument cluster for that matter. The way everything communicates together will make stuff like this hard to do if you want to keep everything working together as it should. I guess one way would be to buy a newer Expedition with a rusted frame or something which is not road worthy, and bring over everything, dash, radio, communication modules, harness and all, but it would be a HUGE project...
Can it be done? Sure, with enough work and access to all parts from a donor vehicle. Is it worth it? Depends, if you can buy the donor vehicle for cheap and have the time on your hands to spend, sure. If not, might as well look for a used 2003-2006 Expy, or 2002 or older if you want the first gen. I don't think the money you would spend on replacing the engine is far from the money you would spend on buying a used car that works.
The old days where you could do this with just minor changes in the harness and electronics are over, these things are so integrated in to everything that it makes it hard to replace the engine with one that was not designed to be in there. Aftermarket PCM's or ECM's could maybe be used, but I think the work on programming these into handling the same as the original ones are complicated and time consuming when it comes to communicating with all the other modules in the car...
Forgot:
The easiest is the find the same type engine that was in the '99. These went up to 2004, before the 3V came in 2005. I think it would be easy to make a 5.4 out of a '02 work in a '99. Possibly the same for the 2nd generation '03 and '04 as the engine was almost the same. For the latter, there may be some sensors and stuff that doesn't fit the harness of the older 1st gen, but it might be possible to swap those sensors with matching ones from a 1st gen engine. Not sure about that, but from what I have read the engine wasn't changed much from 2002 to 2003..