A Naturally Aspirated Custom Tune is $50 if you already have a tuner. If you don't have a tuner, an X3 is $399 and that comes with one Custom Tune. The SF3 is $379 and that comes preloaded to support most '96 and up Fords.
Here are some of the features of the Tuners:
-It has the ability to read and clear trouble codes
-It stores the stock file for warranty repair
-Has high speed on-device datalogging and monitoring
-Adjust shift points and shift firmness
-Set and remove speed limiters
-Can change idle RPM
-Make adjustments for axle and tire size changes
-Spark and fuel adjustments
-And a lot more...
Don't get me wrong, those upgrades are good. But with all these features and no down time, you have to admit it's a pretty good option. Plus, after you get bolt on upgrades the tuner will help with those too.
