Are the LT headers all you've done to the car? In most, if not all cases, adding mods that change the Air/Fuel mixture, i.e. headers, you'll need a new tune. The tune Roush installed is a very conservative tune (EPA standards) and is based on what they do to the car, not what the owner may do...later. My guess is, you need a new tune, running a bit tooooo lean. If you decide to get a new tune, seek out a speed shop that is well known for dyno tunes, the only way to get a perfect tune just for your car.
IF MY CAR WENT AS FAST AS THE MONEY I SPEND ON IT, I'D WIN EVERY RACE