TAW, since when have you been running EFI?
Did you use the Ford ECM or just the guts and Megasquirt? I see that you have the Mass Air on it which leads me to believe you're running an A9L or similar ECM.
Let me recommend that you ditch the Ford ECM, and buy the Megasquirt kit. There's really no reason to be using the Ford especially due to the great snarl of wiring and the lack of user adjustments.
Megasquirt will run with one vacuum line to the ECM. That's all the input it requires. Of course there are other sensors that you'll hook up, like TPS, air and water temp, and even an o2 sensor if you want. Your wire count will drop from 30 or so to about 8. How's that for simple? In addition, you can fine tune it for your type of driving whether it's for economy or power.
OK, megasquirt is bank fire and not sequential, but anything above tickover it doesn't really matter anyway. The only whoop de doo feature of the Ford EFI is the adaptive look up table. This is instead of allowing you to tune it yourself. Oh and the mass air...you can take that out too.