Ford Repair: @003 Ford Mustang GT Idle Problems, negative battery cable, throttle position sensor


Question
I have a 2003 Ford Mustang GT, 4.6 Liter, manual Transmission.
The car is stock, except for a K&N Air Filter, and Flomaster mufflers.
It now has 19000.0 Miles on it.
Somewhere recently it has picked up an idle problem, that has dealership(s) stumped.
When cold the car runs great!
The egine accelerates normally, and the idle drops steplessly when the clutch is in and there is no pressure on the accelerator.
When at "full operating temperature", it is an entirely different story.
If I shift at 2000 RPM, or any RPM for that matter,the idle will hold and even increase to 2100/2200 for ten or so seconds then fall to 1200 RPM for about five seconds, then to 1000 RPM for a few seconds and then finally to 650/675.
I also have a 2003 SVT Cobra that DOES NOT do this.
Since the car is still under warranty, I took it to the first dealer, that sad there were no "codes to pull", but re-flashed the computer with the latest program.
No change!
Second dealer, had a service guy ride with me, who confirmed that things were not right, and said so.
They also could find no codes, but re-re flashed the computer.
Zero change.
The second dealer called Ford and they "Said" that Ford told them, that this was a "fail-Safe" to keep that car from stalling, and that I'd have to live with it.
It is waaaay not right, and I have felt the syncros trying to keep up with the increased RPM, at gear change, particularly third.
I called K&N and tech rep "Leon" suggested that since that engine is breathing better, with the Flomaster mufflers, and the K&N filter that I should disconnect the negative battery cable for about twelve hours and then re-connect to let the computer learn it's new parameters.
Help!
I have never had a car do this, and I have never driven a Mustang (including the Cobra) that does this.
respectfully
John

Answer
John-

  Well..I'm not sure I can be a ton of help, but I'll take a crack at it.  My first thought was that your throttle position sensor (TPS) is out of adjustment.  The TPS' job is to monitor throttle position and translate it into an electrical signal that the computer interprets in order to decide fuel enrichment, timing, etc.  It should ideally be around 0.95 volts (at normal idle).  In the event it tips over 1 volt at idle, the engine will start idleing strange and applying throttle can cause odd results.  The K&N rep you spoke to is just saying what he's supposed to say...but the idea that K&N's filters are so effective they could throw the computer that far off is ridiculous.  However, he might be onto something with his idea to disconnect the battery.  That said, 12 hours is, again, ridiculous.  All you need to do to reset the computer is to disconnect the battery (completely), turn the ignition key to the "accessory on" position (the last position before the car turns over), and leave it for a while and then reconnect it.  Not 12 hours...more like perhaps 20-30 minutes (preferably 30) while the energy is drained from the computer forcing it to re-learn all of the car's settings on the next start-up.  This is a good idea after any modification, really.  Hope this helps.

Steve