I don't have much experience with Ford EFI systems other than what my scan tool will tell me when looking for error codes and EFI type problems but wanted to put some information here for parts and software available like.

TunerPro V5 is an excellent tuner software tuning bin files, data logging and diagnosing regular error codes that will make the the Check Engine light come on. What is really great about this software is it can be used on any vehicle that has a definition file for it, to add to that it has the ability to write your own definition file.
http://www.tunerpro.net/

Parts for tuning including Real Time Tuning is all available at Moates.
http://www.moates.net/