i'm going to play a different angle here. your fuel issue is emulating a problem i've seen before, though yours is slightly different, it's worth a shot.
you are running a MSII-Edis setup. Can you datalog the motor and upload that log for us to look at?
What version of the code are you running? What does the MS show for voltage when this problem occurs? Can you get a stethascope on your injectors to hear if there firing pattern becomes irratic when this occurs? Etc...
I only say this because you've basically been up and down the fuel system till your blue in the face right now. Might be time to take a break and look into a few other potential avenues.
