2004 Gt 4.6

Did you check the injectors? Start the car and let it run for a few min. See if the idle drops to around 550 where it should be. Then pull the plug off one injector at a time. If the rough idle or the misfire stays the same when you pull the connector off the injector, then something is wrong with that one. If you pull the connector off and the idle gets worse, then that one is fine. Do that one at a time with each injector and each coil. That will tell you which one is the culprit. Now once you find the problem cylinder, take the coil, plug, and injector out and switch it with a different cylinder coil, injector, and plug. Then repeat the test. If the problem stays in the same cylinder, then it is a wiring problem or you have mechanical failure like a valve or piston. If it follows the injector, plug, and coil, then one of those is the problem. So once you get to that point you have to swap out the coil, or the injector, or the plug one at a time with a different cylinder. If you swap the coils and the problem stays in the same cylinder, then it is down to the injector and/or plug. That is how you narrow it down. It should only take like 10-20 min.

Idle around 2k usually means there's a vacuum leak somewhere.

In general, expect problems in any car that's experiencing a misfire. Always attempt to resolve a misfire before moving on.

Here's some more information on how to trouble shoot IAC/idle issues.

Troubleshoot IAC idle problems 1996-2004 | Mustang Forums at StangNet

Sounds like it's time for a compression test before doing anything else.

Jeremiah Johnson said:

Hi. Im new to the forum and I am having problems. I have a misfire problem. I have replaced mass air flow sensor, throttle positioning sensor, idle air control. In neutral it will idle at around 2K. Replacing the Idle air control helped with it being sluggish on take off. The miss is still there though. I checked the coils on each spark plug and they seem to get good spark. I at a loss right now. Can anyone help?

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Are you getting a CEL code? The ECU on these cars are good enough to flag a mis fire and it will tell you the bank as well.