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Usually a phone call will get you through to a tech. If they don't know the answer, they will contact someone who does.
To answer your questions:
I am looking to find out just how the SCT fuel mileage chip manages to improve the miles per gallon and does the device leave a fingerprint like the Ford manual states or if not, does the vehicle computer capture a profile/proof of the device which it stores?
No, there is no fingerprint. The SCT returns the complete 100% stock program back to the PCM/TCM. There is an OBD2 readiness code of P1000 that will be present for a few miles and key cyles after you flash the truck with any device. However, it's the same code that you get if you disconnect the batteries. So, it's not an issue.
The Economizer tune has a slight increase in timing at part throttle. The extra power from increased timing is offset by a slight decreased in commanded fuel. So, overall you have a very small power gain and an increase in mileage.
Overall, you will yield as good or better mileage with a general performance tune. With the performance tune, there's also a timing increase at part throttle, as well as a pressure increase. The pressure increase will also help increase mileage due to better atomization and more efficient combustion. However, if you lay your foot into the pedal, it will make great power too.
Either the Economizer or X3 will give you what you are looking for. The Economizer is slightly cheaper, due to only holding a single economy program.