2005 GT Limp mode

My son purchased and used 2005 GT from a non ford dealership about a year ago. Since then he took it back for noise in the rear differential. They decided to replace it with one from a salvage yard instead of repairing the original. On his way home when he hit roughly 75mph it went into limp mode with check engine and maintenance lights. After turning it off and restarting the maintenance light goes not and it runs fine until you hit 75mph. Easy to duplicate. He took it back and they said it was a throttle body (TB) code and that he would have to take it to ford because they couldn't program it if they replaced the TB. Ford too said it was the TB, replaced it and it did the same thing. We had the first dealership verify that the VIN off the salvage differential showed it was compatible and they also said they reused the original sensors. Ford thinks maybe the car was tuned by the previous owner and that's causing the problem. I'm not that familiar with aftermarket tuning but couldn't ford tune it back to factory and fix the problem? Any other ideas would be greatly appreciated!! :banghead:

Yes, Ford should be able to flash it back to factory original spec and apply any released updates. Though at this age of the vehicle they will charge you to do it. I would think a dealership in Sioux Falls would have the software or have access to it.