Mustang idle problem

I have a 2000 Mustang GT 4.6 SOHC with 51000 miles. For some reason after I start driving it will be normal until I go to stop, it will idle at like 2000 or sometimes even 3000 RPM's. If I shut the car off it is good. But when I start driving again it will do it again.I heard it might be a few things so I cleaned my Idle air control valve, throttle body, MAF.I have a off-road x-pipe so the MIL light is on.I also have a intake, flowmaster mufflers, throttle body and intake spacer's. But I removed the spacers to see if it would help but it didnt. Any information would be a huge help.I dont know what it could be. Thank you