You are shotgunning your engine tune. Get it to a dyno shop and do some tuning. If they have a wide band O2 all the better.
94 and 95 computers are notorious for pulling out timing above 4000 rpm. (Ford wanted to conserve some trannies for warrenty issues.) Prior to your gear swap you spent less time above 4k than you do now. You probably have a net loss of torque when running at the strip, due to the timing retard. If your engine is knocking with high octane fuel there is a problem. If you are not using high octane fuel then try some and gradually add base timing. This should help some. The best fix is to chuck the 94 computer for the 89-93 with a conversion kit from pro-m.
Mike
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