De-marko
Dedicated LVC Member
Wow! Good sleuthing. I like hearing that people get there strange issues fixed. 
So, are you saying that the MAF assembly also has a MAP sensor in it? I can believe that it might have an AP sensor, but I don't recall seeing any vacuum lines hooked to it. Without such a line, there is no way it could sense manifold pressure, because the throttle plate is between the sensor and the manifold.
The 04's have a known software issue with the electric parking brake module. There is a TSB recommending that the module be replaced (if the car were still under warranty.) Do you always only get the waring after starting the car? (That is to say that it never just pops up while you are driving around.) Then it usually won't reset until after another start or two? If so, it is likely a calibration issue that comes up due to the combination of software bug and your battery getting a little weak. It can also be triggered sometimes by turning the key back on briefly just after you shut the car down. AFAIK, this is just something that is annoying, but does not lead to actual failure.
You can pull the codes from the parking brake module using a scan tool that has Ford specific codes enabled. One example (purchased with the Ford option) is AutoTap. I think the only connection between the parking brake module and the PCM is the CAN bus, so I wouldn't think the 5V sensor supply from the PCM would be a factor here.
I think the TSB # was/is 17673.
What you described above is an "AP", not a "MAP", so that does make sense.
MAP = Manifold Absolute Pressure.
AP = Atmospheric Pressure (aka barometric pressure).
Some cars have both (somewhat older ones), and others just have one.