I don't think a foot print will cause an issue with the flash paq, but I could be wrong. Best thing to do is call Superchips and ask them what the code means. However, I would try disconnecting the battery while going to the flashpaq website and updating your box. It's possible you may need to reset the ECM or the flashpaq needs an update to program your ECM.

There is only one way to put a stock, unmolested file in the ECM. That is to upload an "as built" file. You can get it from motorcrafts website, if you buy a trial subscription, but the rub is, you have to have a compatible interface. They list several on motorcraft's page, but the prices start at $500 each. So you cheapest route is to go to the dealer.