have an 07 Mustang gt with an airaid cold air kit and airaid poweraid throttle body spacer. also installed is a pair of shelby gt mufflers and superchips flashpaq download. car ran incredible for the first 3500 miles, now in 3rd and 4th gear above 4000 rpm there is a loss of power. the car has not thrown any diagnostic codes so I reprogramed back to stock and the issue is still there. any ideas ?  

Have you checked oil consumption? Spark plugs???
How bout the fuel filter? Do you let the gas o all the way down prior to refilling? Stuff like that..

I would start with the oil consumption first, Stangs suck up a lot of oil at high rpms.