A misfire at idle that smooths out at cruise is ALMOST ALWAYS caused by a vacuum leak. Take a hard look at your fuel trims at idle. If the Bank 2 Long Term Fuel Trim is more than + a couple points higher than the Bank 1 trim, your problem is most likely a vacuum leak. If the Fuel Trims even-out while holding the engine at 2000 RPM for about 20 seconds, then a vacuum leak is DEFINITELY your problem. I would suspect a leaking lower intake gasket leak because an upper plenum leak will normally affect all cylinders.
It sounds to me that your problem could be the pcm you can check if the problem is the pcm by checking with a test light the current in the coil pack connector. there you'll find 3 cables that the light will blink an one that the light will be steady, you will look for the blinking light if u see any difference in the brightness of the bulb in one of the wires that send the signal to the coil pack, then you should check whether the wiring of the computer to the coil package is not open or shorted with a multimeter. if u find that the resistance in the cable is less than 5 ohms then your problem is the pcm
You didn't state year or motor size but 28 psi seems a little low for fuel pressure double check specs
other than that i would lead to pcm
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DTC P0301 Cylinder 1 Misfire Detected
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DTC P0302 Cylinder 2 Misfire Detected
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DTC P0303 Cylinder 3 Misfire Detected
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DTC P0304 Cylinder 4 Misfire Detected
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DTC P0305 Cylinder 5 Misfire Detected
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DTC P0306 Cylinder 6 Misfire Detected
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DTC P0307 Cylinder 7 Misfire Detected
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DTC P0308 Cylinder 8 Misfire Detected
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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Have you swapped coils? After market coils are not very good.
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