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I bought a '95 F-250 with the engine out. The engine it came with was out of a '96 F-250, will I have any problems running this engine in this truck if I used the trucks wiring harness?
If both are heavy duty F250s (over 8800 GVWR) then they will both be OBD-I and should interchange without any issues at all. Even if the 96 is OBD-II, the engine itself is the same as what was used in 95 and can be swapped easily, although some sensors may need to be changed to what was used in 95. Again, this won't be a problem as long as the 96 engine is from a truck over 8800 GVWR.
As long as you just use the 96 block with your old 95 intakes and your old 95 engine harness it should work fine.
Also use your 95 PCM Computer and its wiring.
I'm thinking the 351s from over 8800 gvwr trucks had air injection feeds to the exhaust manifolds, but I don't know that for sure. This might be another way to tell what truck it is from. If any of the sensors don't match, it would probably be just a matter of purchasing the needed sensors for a 95. Without seeing what you have I don't know for sure what, if anything, would need to be switched.