There was a recall for the 4.6 computer to be reprogrammed by Ford in 96. There is quite a noticeable difference between engines of the GT and the Cobra. For starters the valve covers for the Cobra are twice the size of the GT's. Try and reprogram the computer by unhooking the battery for 30 min. Then hook it back up and let the car run for about 10min to learn again. It'll also take a little bit of driving around (easy driving) to reprogram itself to engine idle speed, etc. A code may have popped up in your computer and the computer maybe holding the engine back. Take the car somewhere and have the computer scanned to see if any codes pop up. For instance, if the previous owner put on an off road h-pipe your check engine light/system would turn on and the computer would reduce the power of the engine to get the correct emissions. The previous owner could have removed the light bulb so he wouldn't be looking at the light all the time. I know of people that have done it. The new OBD-II computer is sensitive to stuff such as the exhaust modifications cause it's alot faster than the previous EEC-IV computers of the 5.0. Get the computer scanned. It should tell you whatever could be wrong with your car.
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1996 Mustang GTS
K&N, removed air silencer, 3.73s, turndowns after H-pipe (no mufflers)