Subbed.
Always worth while to have a system that will let you diddle with your settings on the fly or on a dyno (get professional help tho).
Ive seen things like this before, usually work well.
As to the fuel issue, wouldn't it work just as well to upgrade the entire fuel delivery system, pump, lines (if needed) rail (also if needed, need to get someone with more tools and toys then me) and bigger injectors, then tell the computer whats what? This is what the Taurus owners group I used to belong to looked into. They put a bigger fuel pump, braided lines, bigger injectors on to the 3.0 twin cam motor and after a good dyno tune were able to squeeze out a significant chunk of power out of the motor. Dont ask me how much, its been...years since I was there (my 2003 SES Sport ate both cats, EGR valve, all 6 injectors and sparkys and damn near siezed the motor when fuel, ethanol, carbon, and GOD knows what else flash fried 500 miles from home....SNARL), but it wasnt too expensive.
Thats my hesitation with the AP and CP-E stanback, they are both too expensive for being locked into certain sets of stuff.