I'm not familiar with the SCT X3 device, but you should be able to navigate through it's various menus and prompts and adjust shift points and firmness yourself. I'm not sure how the shift points and firmness could get any weaker than how Ford set it up - my bro in law has a bone stock '03 GT auto and maaannnnn is that thing ever a slushbox lol. From a dead stop, stomp the happy pedal and it barely chirps the tires; 1st gear is completely underwhelming and goes into 2nd too early. Don't get any real acceleration out of it until 2nd, which feels nice and revs well past 5500 before going into 3rd.
If I had an auto, first thing I'd do besides adjusting it with a tuner is J-Mod the trans. For more info on that, type "J Mod 4R70W" into Google. I'd also do 4.10's or 30's and a 3000-3500 rpm stall, but that's another conversation entirely.
I have 4.10s, but they were installed by a pal year ago, and they howl pretty bad. I have new 4.10s (bought with the tuner) to swap them out, just need the time and money to get them installed properly.
I've been wanting to do the J-mod for years, and that will probably be a follow up project after getting the gears reinstalled.
My only concern with the custom tunes right now is that it feels like the shift points are... I don't know... chuggy. If I'm driving WOT, its pretty awesome, but I do a lot of DD with this car, so hitting chuggy shift points while doing 35 m/h feels awkward. I don't know if that's something I just need to get used to, or if maybe my rear end is jacked up from having gears improperly installed for so long, or if the tune is just too aggressive. I figured I'd wait till I had the new gears installed before bugging anyone at AM about it.
I'm also sort of disappointed that the tuner didn't fix my speedometer. Looking at the questions and answers on AM's website for folks who have a 96-98 GT makes it sound like the tuner will fix the speedometer, but I found out through customer support the other day that this isn't the case. That's not a really big deal... I've lived with an off speedo for years now, but it sort of calculated into my buying the tuner in the first place. Guess I'll just have to save up for a Speedcal. Other than that, I really dig AM as a company, and think the tuner is pretty cool.