There are five types of PATS implementations from Ford (A, B, C, D, E).PATS initialization is generally performed after programming.
The A or D version of PATS does not store the key information in the PCM, therefore NO PATS KEY RELEARN IS REQUIRED after programming.
The B or C versions of PATS store the key information within the PCM and MUST be transferred to the new PCM, or relearned on the vehicle after the new PCM is installed.
The E version of PATS also stores the key information within the PCM, but CANNOT be transferred to the new PCM. This type MUST be relearned on the vehicle after the new PCM is installed.
99-04 use pats version C and must be transferred to a new pcm.... The key transfer to a new pcm will not over rite any engine management software. The key data is just a stored code on the pcm and can be done with a tech II at the dealer.