So if you are running a complete Aeromotive fuel system with A1000, I assume you are not running stock injectors or a stock mass air? I can't see why you would have that fuel system without a need to support other things. I know when I changed all those items, my car wouldn't run on a stock computer either. I needed a custom chip to allow for all the other changes. Are you running a chip? Did you try to add that chip to the new ECU? Even though the computers aren't much different in stock form, your chip was probably burned specifically for that ECU. You might have more issues now, if you tried to add that chip to a different ECU.

PS. If you did swap those chips around, then I would only be able to point you to Rob @ Fordspeed. Trust me when I say, he is worth getting a trailer and taking your car down to him.