2003 Ford Mustang V6 3.8L gets around 12mpg and seems to shake a bit when started cold and has a bad rough idle when warm

Hey everyone I've tried so many things to get this fixed. When I start it up in the mornings the car will shake a little bit, but when I drive around for a bit let it get up to temp and run it for a bit. Then I'd stop at a store or something for around 15 or so minutes and I'll come back to start my car but the rpms will drop down to about 500-700 and want to die out. I recently cleaned the maf sensor, put a new cai, new radiator, new water pump, oil change recently, new spark plugs, new spark wires, ignition coil, (my alternator was tested and it failed) new alternator, ran seafoam through gas tank and through the throttle body (not at the same time and not within the same gas tank). I'm out of ideas of what to do next. Any help would be great, I've touched just about every bolt in my car it feels like. Also only has 75k miles
 
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Do you have an ODB2 scanner? If you did it might make short work of your problems. At the very least it will give access to vital trouble shooting information.

Take a look at the ODB2 mode 6 misfire data to find out WHICH cylinders are misfiring.

ForScan ODB2 scanner w ELM327 USB
https://www.stangnet.com/mustang-forums/resources/forscan-odb2-scanner-w-elm327-usb.57/

Are you POSITIVE that the complete charging system is in tip top shape? Not just a new alternator?

Howto perform charging system voltage drop test
https://www.stangnet.com/mustang-fo...perform-charging-system-voltage-drop-test.56/

Troubleshoot IAC idle problems 1996-2004
https://www.stangnet.com/mustang-forums/resources/troubleshoot-iac-idle-problems-1996-2004.13/
 
need to check the MAF, MAP and IAT sensors. the pcm utilizes all of these to know how much fuel is needed in the cylinders, if any of these are faulty or dirty you will get an improper reading which will lead to idle and driveability issues
 
Go to your nearest auto parts store and have them run the codes. Write the codes down and post here. It's completely free to have them do this. Then we can provide more help. We have no idea what's going on and making guesses without more information is pointless. If I had to assume you probabaly need to replace your intake gasket. Air entering past the throttle body will cause your pcm to read lean and add more fuel causing horrible gas mileage and low rpms at start. Could even make it stall. Couple that with a vacuum leak and you will easily have a rough running car. The intake gaskets should be replaced every 50 k miles in my opinion. Most don't go bad before 100 k miles but preventative maintenance to keep the car running great reduces issues for other problems to arise down the road. In your case fouled spark plugs from too much fuel or bad oxygen sensors repeat combustion in the exhaust. Just to name a few examples.
 
My 2000 base v6 does the exact same thing. It isnt showing any lights on the dash though so would an OBD2 still pick up codes? Ive already ran B12 through the system once, and replaced the fuel filter, still does it though, only when the engine is warm and i try to start it after 15 mins or so.
 
My 2000 base v6 does the exact same thing. It isnt showing any lights on the dash though so would an OBD2 still pick up codes? Ive already ran B12 through the system once, and replaced the fuel filter, still does it though, only when the engine is warm and i try to start it after 15 mins or so.

A leak down test would solve these issues. When you have air entering past your throttle body, finding the culprit is extremely hard but can be done at times. No cel lights and rough starts after the engine is warm is bad seals(usually). When the car is cold the seals are expanded providing a better sealed system. So starts up fine after setting for extended periods of time. Once the motor gets warm these seals contract because they are rubber, which allows un-metered air into the motor. Once this un-metered air exits the exhaust stroke through the headers the upstream oxygen sensors read a lean condition(this doesn't throw a code) and lean means not enough fuel, the pcm then calculates how much more fuel is needed and the injectors are now spraying more fuel than needed since the pcm did the math. Its technically flooding the car out so when you turn it off and try to turn it right back on its hard to start because there is too much fuel in the combustion chamber.