The EPA has a FAQ about the federal emissions warranty--the PCM is most definently covered for 8 years/80K.
Also note that if a TSB covers the reflashing, it says "warranty coverage: applicable under the terms of the bumper to bumper warranty and the federal emissions warranty" at the bottom of the TSB.
I would take this to mean that ANY reflashing ot a PCM is covered under the warranty. Also of note is the fact that Ford does NOT want their dealers to replace the PCM for a problem, it is to be reflashed unless the PCM is damaged or cannot be flashed. There's a TSB out about that too.
