My Feeling is they reflashed the car to stock. That is, the programming in the ECU from Roush is no longer there and you're driving a stock programmed car.
I've been hearing rumors that this is becoming more common, in part because of emissions updates available. Thing is I don't hear that Ford is asking customers if they can reflash the cars. They just do it.
Now I may not be right, I sure hope I'm not, but it's something to call and ask about.
Anything mechanical just doesn't seem to fit.
Don't "think outside the box".
There is no box.
Do it correct, or do it twice.