HELP 2005 Mustang Gt PCM, ENGINE FAILSAFE MODE

So this last Friday I traded my old car for a 2005 mustang gt. It was originally an automatic, but was converted to a manual. The guy said that it should drive fine but all I have to do is take it to Ford and have them reprogram or flash the PCM back to a manual tune. Was the guy lying to me or is it really this easy? The car is in an engine failsafe mode and I want to know if going to Ford will fix it and if the car will ever be able to drive to its full potential.
 
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