I'm not going to diagnose your issue, but here are a couple other things to consider:
Which brake switch input are you looking at? There are two. A brake pressure switch input and the regular brake on/off switch input.
The brake pressure input to the PCM needs to be hooked up. This is a normally closed sensor on the front of the master cylinder. An open circuit will cause the input data to show that the brake pressure is high (like the pedal is depressed).
As far as the brake pedal position switch (Brake On/Off) is concerned, what do other modules "say"? The ABS module uses the same input as well as the GEM. The PCM needs to see ground when the brake pedal is at rest and the switch is in the "not applied" position. An open or 12v will cause the PCM to think the brake pedal is depressed.
Things to try (in accordance with which switch input is having the problem):
Disconnect pin 92 from the PCM. This is the brake pedal switch input. Use a test light to determine if you have voltage there. If you don't, use an ohm meter to check for continuity to ground (brake not applied, of course). If you have any spare EEC-V harness terminals, you can plug one into cavity 92 and ground the end of the wire. Check the data and see what it says at that point.
If the pressure switch input is the problem, short the two wires together that go to the brake pressure switch using a paper clip or something to bypass the switch. I just thought of something....if you have the Ford recall done that fuses the brake pressure switch and it happens to go open, the pressure switch input will be "on" all of the time too.
