Phatcat...have you looked at the new FAST yet? They are amazing with what they will control. There is no way in this world I would attempt this using the factory ECM. It is WAAAY to sophisticated to integrate. There are just too many other inputs and actuators needed that your vehicle won't have. Remember...in your '66, this will be nothing more than a fuel injected engine. You only need to control the variables to make it run properly and the FAST does that extremely well. Things like Variable Valve Timing, Drive by Wire, etc will need to be eliminated...but that is easy to do. Richard Holdener is using the FAST to run the new Mustang 3V on the dyno and it has those same features. He just eliminates them. Off the top of my head, you will need a MAF, an IAT, a CTS, a TPS, an IAC motor, O2 sensors, and of course the injectors. Those items with a good fuel and timing map in the FAST should allow you a very smooth running engine.
I've done several swaps of late model EFI engines to early iron. Without a doubt, the most difficult part of the swap is building the fuel system. With this swap, the only thing I would consider is a return style system and eliminate the FRPS and the returnless system. This may very well call for a new or modified fuel rail that you can adapt a pressure regulator to. But in the long run, you will be very happy you did. There are companies that offer fuel rail logs that you can drill and finish to your own injector spacing requirements if necessary.
I think this is a GREAT project! Have you got past the problems of mounting it in the car? What trans are you going to run? If you run the factory 5 spd auto, you will need computer controls of that too. I'm not sure what FAST has to offer in that department. Adapting to an AOD or a stick may be a much better route. Good luck and keep us posted!!