Its been awhile since I've been into a 3rd gen but I'm finally bought one again and loving it until I started having issues. I drive the car every day to and from work its only about 6 miles total. In the mornings I've been having issues the past few weeks. When I go to start the car the engine fan on the driver side turns on and the service engine light does not come on. The car starts and runs just very poorly idle is about 750rpm. While driving it runs rough with poor throttle response, it clears up after about a 2 miles of driving and runs great. When it clears up the SEL light flashes and goes out. After I get off of work, I go to start the car SEL turns on, no fans car starts and runs great. The next morning the fans come on and runs rough again. I tried to pull the flash codes and no codes flash not even the diag 12. When it runs good i'm able to pull the flash codes but only flashes 12. Sorry this was long winded just trying to give out as much info as possible. Thanks

 

Sounds like it could be a bad ecm

 

You could try tapping on the ecm hosing with a screw driver handle to see if the engine running condition changes.
sounds like a cracked circuit board or a bad solder joint.

 

Well went out to the car this morning it was running rough, tapped on the ECM like you suggested runs great. Thanks for the help do you have any suggestions on where to get a good ECM?

 

Not very many remanufactured companies. Used one in the wanted classifieds 1227165 is the service number.
or see what RockAuto has I think it might just be cardone.