The 97 and newer Explorers and Mountaineers have the 5.0 motor in them. The intakes on these motors flow very well. Comparable to the cobra intakes, but not better. They flow about the same. The Expl. and Mountaineers do not run a smog pump and the holes for the fresh air tubes are not in the heads. To keep this emmisions legal you might be able to drill the holes out. The exhaust manifolds are not the same but there is an aftermarket company producing headers for the GT40P heads to go in the Mustang. Your idea will work very well but it might take a little more messing around then its worth. You might want to stick with the short block and use the older style heads and intakes. Good luck
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