Fuel Return
Kwikkordead, I've been looking at your setup and doing some research (I have the Ford Tech Service Info on CD-although it's for 2001-2002). I came across the part that states that the fuel pressure regulator sends all unneeded fuel (excess fuel under pressure above 75 to 80 psi[2001-2002, other years pressures may be different], back to the fuel tank through the return by bypassing the filter. Since the return is connected to the fuel filter assembly, it must make a "U" turn inside before going through the filter. What this seems to be (to me at least) is that after going through the filter assembly, all other fuel (the fuel in the rails of the heads) will be at a lower pressure because of the pressure loss across the fuel filter. Even the slightest drop in pressure will cause a return line from each head's fuel rail to stagnate (not flow) because of the slightly higher pressure of the fuel coming directly from the filter housing. (you're getting flow now as you're evaluating the problem because the fuel is only fighting atmospheric pressure- 0 psi). This is even before calculating pressure loss from use through the injectors and from piping configurations and restrictions. I know that it could probably be done, maybe with a small auxilliary fuel pump or something, but then there's the risk of disturbing the readings on the sensors within the heads, and from the diagrams and descriptions from Ford, these are substantial.
Any chance of finding the vacuum leak that's allowing the air into the system?
These are just my thoughts and with these and a dollar, you can get a cup of coffee in most places.