I have an 03 Mustang GT. I picked the car up used from a dealer. Little did i know i bought a car full of problems. Come to find our the owner before me had a supercharger on it, and once he traded it, he took it off and went back to stock engine. I have had a “Cylinder 3 misfire detected” code on since about the time i bought it. I have replaced spark plugs, fuel injector, moved the coil pack to see if the code followed the coil pack, and i have had compression and air leak tests run and it was perfectly fine. I still do not know why the light would be one…the car runs perfect…
You might try swapping the crankshaft and/or camshaft position sensors.