I have the SCT and I love it. I bought mine used and unlocked on ebay for $150 (vs $400 new). Then I had a custom tune made and emailed to me. I have the 93 power tune and a 93 economy tune. If I make some upgrades to the truck like exhaust or intake etc. then I can have a new custom tune made- or I can bring my truck to the local dyno and they can custom tune it directly on the dyno and get a few more HP out of it.
If you buy an over the counter tune file you won't get as much HP out of it. The place that wrote the tune file for me has supposedly a great reputation for Expedition tuning and the guy has a long list of files that he custom made on his own dyno. I just told him what mods I have and he sent me the best choice.
I know that with the SCT tuner I can modify my shift points, the idle speed in gear and also in neutral, I can change shift pressure in each gear, adjust the speedometer for tire sizes, ignition timing at various rpms, mixture at WOT, and a few other settings.
It's pretty cool that I can change the program to match what I'm trying to do. For instance if I want to tow something heavy I might raise the shift pressure a little bit and increase the timing at low RPM's. If highway cruising and saving some gas, I'd use the economy tune and pick up 1 or 2 mpg.
With the highest shift pressure it will sometimes bark second gear on dry roads, and spins going into second on wet roads. There's no real reason to have that much pressure but at least the ability to control it goes that far.