csx4910,
I feel your pain and know your frustration.
Aftermarket EFI can really try your patience, but when you get it right, and you will, you will be very happy w/ the drivability.
I have been down the aftermarket EFI road more than once and have to tell you honestly that the key to making it work correctly is in the software and the tuner.
I can also tell you that even though as others have said that the Roush programming is proprietary, it can be gone around and reprogrammed if necessary.
Dave at AutoTrend EFI is an expert in these areas and has my injected Boss motor running like a top on Accel Gen. 7 software.
At the very least, I would suggest that you give him a call and bounce your problem off of him. (530) 642-0999
Check out his website if you get a second
http://www.autotrendefi.com/
I wish you the best of luck.
Chris
Send me a PM if you would like to discuss any further