I'd probably stick with what you have now and put a windage tray, better oilpan, and upgrade to roller tip rocker arms. Are you keeping the induction system from the 97 Mountaineer or changing it from the F150s engine?
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Yes keeping the upper and lower GT 40 intake
With the GT 40 intake, I would just get my little die grinder out and port it out a little. Nothing fancy, just knock off the sharp mating edges and any casting flash. Maybe a bigger throttle body on it.