There could be several problems. I'll start with the easiest to hardest, First a bad spark plug next a spark plug wire then next thing to check is the coils it getting fire? By pulling the plug wire off #3 and putting a screw driver in it get it close to ground about 1/4 inch and watch if it arcs, if it does then it could be one of the following. Fuel injector going bad on #3 or valve adjustment on #3 so you can check the plug the plug wire and the coil and if you had a noid light you could check for injector pulse if it has a pulse then injector may be failing mechanically or electrically let me know if you need more help and please rate me if this answered your questions.
2004 Marauder and 2003-2004 Mustang vehicles built before 12/19/2004 equipped with 4.6L 4V/5.4 4V engine may exhibit a runs rough, lacks power, and engine misfire, prompted by a MIL light and DTC codes P0301, P0302, P0303, P0304, P0305, P0306, P0307, P0308, and P0316.
ACTION
Diagnose engine for engine misfire concern. If diagnostics determine an engine misfire which is characterized by leakage through exhaust valve(s), only replace the affected cylinder head(s).
SERVICE PROCEDURE FOR VEHICLES WITH RUNS ROUGH/MISFIRE CONDITION:
1. Perform relative compression check on all cylinders. If abnormal, check cylinder leakage and actual compression for "low" cylinders refer to Workshop Manual (WSM), Section 303-00.
2. If leakage/compression check indicates a valve train concern, per valve train diagnostics in WSM, Section 303-00, replace cylinder head and cam assembly, pipe plugs and timing chain tensioner, per procedure outlined in WSM, Section 303-01.
3. If cylinder leakage and compression tests are inconclusive, perform misfire diagnostic, per TSB 05-22-8.
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