It depends on your driving requirements. I drive 600 miles a week on the highway, so I went with the 3.31 setup. Great step from the stock arrangement.
If I was driving mostly city, and wanted quick start accelleration, then I would have gone with a taller rear gear.
Only you can decide what's your daily driving? Mostly city? Mostly highway? You want quick off the line starts?
Another thing to keep in mind: anything over a 3.31 is going to require a tuner to alter the speedometer reading. Ford can flash the ECU/PCM if you go with a 3.31. Anything over that will require a tuner to compensate for the speedometer being off.