Have you done a gear swap to the rear by chance? With 3.27's, a '99-'04 Mustang will top out in 4th gear, but not in 5th. But....if you swap out to a set of shorter gears like 3.73 and higher (numerically) you'll run out of gear in 4th, but will still lack the power to pull it in 5th.
My old 5.0L was faster in 4th gear with the stock 2.73's in it than it was with the 3.55's. It would burry 1:1 4th gear ratio pretty easily, but still not make enough power to pull the .68:1 5th gear all the way out to redline.