2003 Mustang GT Problem!!!
 

Engine Misfire Detected on Startup (First 1000 Revolutions)
Cylinder #1 and #2 misfiring.
I literally just replaced the plugs Friday.
I know there's a chance of it being coil packs, but wouldn't the coil pack itself throw a code?? (They are Coil-Overs) They cover the spark plugs with boots. No wires.

I have Flomaster 60s attached to my exhaust, so when it's idiling and etc it makes a deep chugging sound? (No not like the actual flomaster sound)

Good chance that it's the coils going bad. I usually just buy a set of cheepos off ebay and call it a day.

Agreed, they are coil on plugs. They just go bad. I would look to see if the boots are torn up or have any holes in them. It's possible you tore them or it just had a weak spot and the spark found it. When 1 cop goes bad I go on eBay and buy a set of aip cops for cheap. If you know the spark plugs are good I would just shot gun it and get a new set of cops. I rarely see fuel injectors go bad.

An easy way to determine this is switch those two to different cylinders' im the miss changes to those cylinders then its the COPs

Unfortunately NO. The COPs do not have a sensor that tells the pcm they are bad. The pcm interprets a signal from the crank sensor and can see a miss on any given cylinder because of a change in pulse width at the crank sensor on those cylinders. Pcm doesn't know why its missing , only that it is missing. It could be fuel spark or compression issues. Any thing than interrupts the normal pulse of the crank sensor.

Uberstang is correct, before throwing money at it and just buying parts you need to diagnose more closely what is going on. By moving the 2 suspected COPs over to the other side . Clear codes and drive till it comes back. If the miss follows the COPs then you have found you problem. If the miss continues on those same 2 original cylinders you need to look deeper for the problem. To much or not enough fuel cause by malfunctioning injectors ( highly unlikely ) or not enough compression ( blown head gasket) Since the #1#2 cylinders are next to each other a blown head gasket would not be out of the question.

If it was a headgasket probably would of been signs when changed the plugs

Why does everyone keep saying buy cheap COP's? Diagnose the problem correctly and replace that one with a quality replacement. My COP's have over 160K on them and they're all original.

Okay, here's what I've done so far.

I switched #1 and #2 cylinder coils to #5 and #6
The actual order they fire in is 1 3 7 2 6 5 4 8
Check engine light hasn't came back on since I cleared it with my OBDII Scanner

So would that mean I should just go ahead and replace them? Because I'm confused, I thought if the coils were bad then after you clear the check engine light, usually they come back on if it's the coils

Give it a few days. If it's the coils then the misfire will come back to cylinders 5 and 6 since that's where you moved the coils in question. If the misfire stays at the same cylinders then you need to look at the coil connector for wear.

Ahhh **** it. I'll stick to my 79' 360 Crate Aspen R/T if this **** doesn't fix after I replace the coils lol.