What do you mean by "nothing is the same" ?
Is it a V6 also? If so, I would try to move stuff over from the old engine so that you can use the existing harness and PCM. That would be the easiest way. In other words, move the intake manifold and sensors from the old engine to the new one, so that you can use the existing harness and PCM.
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11 Mustang GT (Street Car)
87 Grand National (Race Car)
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