keep the ENTIRE wiring harness from your old 4.0 and stick it on your new 4.0 when you put it in....that's about it, I've heard the odd sensor like your 02 sensor may be different so when it doubt just use your old one.
95tm head casts and newer have the fast burn chamber, but they also have a deeper dish piston which kept the compression the same to match those heads.
didn't find a true answer but quote "All of these engines had the same compression ratio whether they came with the original heads with the open chambers or the newer ones with the heart-shaped chambers, so they would seem to be interchangeable, but the computer calibration that was used for the old-style heads with the open chambers will not work with the newer heads with the fast-burn chambers. In fact, "It will burn the engine down in a few thousand miles," according to a Ford engineer who worked on this engine program."
Most likly timing, the four liter used 4 different cams throughout the years i would assume the pcm's are tuned to them and by right should match. http://www.babcox.com/editorial/ar/40123.htm
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