I just got my SHO back a week ago from my dealer after they had the car for an entire month. I was having a grinding issue in the rear end.
Before taking the car in I reflashed to stock. the dealer confirmed the grinding sound but could not confirm the cause or exactly what the grinding was. after going back n forth on the ford hotline, replaced a module, PCM and reprogrammed it, it still did not fix the issue. the dealer then asked if i still had the stock air box cuz i did have an airaid cai on the car, i droooed of the stock box, dealer installed it and still problem not fixed. the dealer requested numerous times for an engineer to come and look at the car, instead they gave permission to the dealer to replace the entire rear end. problem fixed.
not once did they ask if I tuned the car.
now I have an issue with reinstalling the tune cuz of the new PCM. dealing with Torrie on that issue now. I have a new laptop with windows 8.1 and cannot get the software driver to install. Friday night drags coming up this Friday, I hope this gets fixed quick.
Hope this info helps.