Well, I can finally put this to bed. I got my vehicle back today! I got a little suprise when I walked in though. The service manager, the operations manager and some other upper managment guy were all there waiting for me. The service manager told me my vehicle was all done and Ford covered everything except for a melted transmission vent tube (which they blamed on the downpipe) BUT, and there was an errie pause, he said, "we know you are tuning your car but Ford was unable to prove it"! That is what took so much time. Then the operations manager spoke up and said "we see this all the time with these high performance vehicles. Had the guys at Ford been able to prove your computer had been tampered with, you would have been on the hook for around $12-13K and your extended warranty would have become null and void." Of course I still denied it to the end. If I had to pay for it then so be it. You accept that as soon as you load that tune in the vehicle. I was prepared to fork out the $5,900 to this other guy to get it fixed. At least it's done, so far there are no issues and I have somewhere else to take it if I have an issue in the future.