You will lose torque by using a 3" exhaust on a stock engine. Torque is what gets you off the line quicky and makes a Mustang fun to drive on the streets.
Even 2 1/2" exhaust isn't good for performance until you get up past 300 Flywheel HP. Stick with the 2 1/4" stock setup and save some $$$ and keep the low end torque.