Nightkids,
You definitely want to go with the SCT Xcal2, as people mentioned. This is especially true for owners of the automatic trans. For around $400 you get a bunch of performance enhancements which include...
1) An immediate and *noticeable* gain in HP and Torque, even with the "lower-octane" tunes (87 & 89). Check the dyno at alternative auto to see the difference.
2) Elimination of the wide open throttle (WOT) delay. Ford programmed an (approximately) 1.5 second delay before full throttle is applied. If you floor the pedal from a stop, you only get about 1/2 throttle for the first second or so. Supposed to protect the drivetrain, but the auto is the same one used in the GT which has 320 ft/lbs. It can even handle modified GT's power output (up to a point), so there is really no reason for the delay. It's extremely annoying. With the WOT delay gone, you will be able to spin the tire (only 1 until you get a LSD).
3) Reprogramming of the auto's shift points to a more aggressive setup. This alone can/will improve your acceleration runs by allowing the engine to rev higher before shifting, plus, making the shifts quicker/firmer. Stock, the clutches/bands slip a bit to make the shifts smooth. The tuner can make the shifts immediate and firm. This may even be better for the lifespan since slipping a clutch tends to wear the plates faster.
4) Recalibration of the speedometer to accommidate different size wheels or tires. You will need this if you get plus size wheels/tires.
I think there are additional benifits, like data logging (to aid in performance analysis), engine diagnostic functions, etc. As far as engine performance is concerned, this is absolutely to best bang-for-the-buck. Plus, you will need one to maximize your performance gains from other mods (CAI, exhaust, head work, etc.)
However, all "tunes" (the computer reprogramming provided by the Xcal2) are not created equal. Make sure you get one from Lidio, Doug or other "StangNet-approved" dealer.
Good driving pony brother!