The engine is a bolt in. The wiring and computer system for the newer engine and getting it in place is the problem. I believe the 4.0 does use a different starter and flywheel/flexplate, so keep them together during the swap.
FYI, you need an engine out of a 97 or older because 98-00 used a different fuel system and you’re already going to be doing a lot of “make it work” work. Ideally you’ll get the engine harness and computer out of a 90-92, it will be the closest to what you have, which isn’t saying a whole lot. You are going to have A LOT of wiring to be done.
I started this with my 88 years ago, back before there was much information available and it was a nightmare of wiring. I don’t mind wiring, but it was a lot to deal with and I was having trouble devoting enough time to the project. So it sat a lot and then my 89 choptop needed more power than the 2.9 that was in it could produce so the motors got swapped because I didn’t really need a 4.0 for my 88. The wiring becomes a lot easier in 89. One thought that I did have before going the route that I did (because I didn’t want to swap the first gen dash either) was to get a second gen dash harness and see if I could make the harness adapt to a first gen dash, it may or may not simplify the wiring work.
The easiest route would be to use a wiring harness and computer from either a 90 to 92 Ranger or 91 to 94 Explorer. To go this route you will also need all of the sensors and such from the same vintage of vehicle, and, depending on the year of 4.0 you have, you'll also need to swap the injectors and fuel rail. It will not be plug and play, wiring wise, but it won't be too hard. Going to an OBD2 setup would save you the trouble of swapping everything but you'll still need to wire things and it will be much more of an involved process.
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