TwizzleStix
Pudendum Inspector aka FORZDA 1
One thing first, "the pedal commander does not access the PCM".
It only amplifies voltage going to the Throttle Body.
The TB voltage range is 0 being closed to 5 volts wide open.
So lets say you set the pedal commander to it's highest setting,
when you depress the go pedal a quarter down it will send 3 to 4 volts to the TB instead of variable 1 to 1 1/2 to 2 volts.
I have a question, are you guys running a Tune to go with the pedal Commander?
A proper Tune will eliminate/turn off the 3,500 rpms safety feature before opening full throttle.
Incase you didn't know, Ford has a safety built in the OEM Tune to not allow full throttle till 3,500 rpms.
So if you turn up the pedal commander to high (like stated earlier)
The Pedal Commander will throw the TB plate too wide open before 3,500 rpms.
The PCM is going to think something is wrong.
You've made several statements here that I believe are incorrect. The PC definitely connects directly to the ECU(PCM) from the Throttle position Sensor (TPS) and the ECU sends the Electronic Throttle Control (ETC) commands to the TB itself. It MUST work this way because the ECU can and does regulate the ETC.
For me to be SURE, what year(s) are you talking about?