Making Changes to the PCM Calibration
WARNING: This page is about a different car, the 2012 Ford Pickup, 2012 Ford F550 Super Duty, 2012 Ford F450 Super Duty, and 2012 Ford Cab & Chassis. However, it is still accessible from the selected car via links, so may be relevant.
At certain times, the entire flash EEPROM needs to be reprogrammed. This is due to changes made to the strategy or calibration after production. Refer to PCM Reprogramming on the scan tool.