Is the Check Engine Light on? Even if the Check Engine light is not on valuable information may be stored in the computer in your car that may hold useful information in diagnosing the problem with your Mustang. A scantool is needed to interrogate the information stored. Your engines problem could be a loss of fuel pressure or supply volume, an exhaust restriction, or the car's computer has seen a fault and put the car in a "limp home mode".
Its hard to guess without being able to drive the car and experience the problem first hand.