What are your edis settings?
Under ignition options I have Ignition input capture set to rising edge, cranking trigger is calculated, coil charging scheme of course EDIS, and spark output is going high (inverted)
Also, what kind of plugs are you running in the motor? I was running NGK copper plugs until I started reading about the Ford EDIS system.
All of the factory ford guys that have edis swear you must run double platinum plugs (the kind with a platinum tip on the electrode and strap.
As a matter of fact Ford called for different part number spark plugs in each bank on some vehicles. It has something to do with the polarity reversing in the coils and the way electricity flows in the plug.
Anyway, I switched to Denso double platinums and the car was a different animal. Idle, cruise, throttle response and power in boost (16psi) improved greatly. And I even thought it ran pretty good before.
I would highly reccomend double platinum plugs if you are running edis and msII.