If you buy an SCT/SF3 or the SCT/SF3 X3 from American Muscle for 379.99 you will get 3 canned tunes an 86 89 and 91 or 93 octane and with the SF3 you also get 3 custom tunes,and you will get FREE tunes for life, so every time you add something to your car, you just call and tell them what you have done and they will write you up a new tune and Email it to you, usually in 24 to 48 hours, FREE!! You said you have the
K&N CAI, I do not know if that CAI requires a retune or not, my C&L Racer does, maybe thats why your car is running poorly.
I ordered a C&L Racer CAI today and called Bama, talked to Chris Rose and asked him to update my 93 Race tune and add my new C&L CAI to the tune, and within 2 hours he emailed me my tune for free!!
Let me tell you how much the 93 Race Tune has done as far as power goes for my car, let me first tell you I have the same car as you, a 2006 GT (automatic) bone stock except for the 93 tune and
Magnaflow Magnapaks, pretty much the same as you (except you have the CAI and I do not, yet, mine will be here Friday!!) I had the 93 Performance tune and it there was a noticeable difference in power, on a scale of 1-10 I give it a 4, but I had been doing research and was reading what a lot of people were saying about the 93 Race tune, so I called Chris Rose at Bama and asked him to write me up a 93 Race tune and told him I had added the Magnapaks since my last 93 Performance tune, so he said no problem, I will write it up and Email it to you as soon as its done, and 48 hours later, boom, in my inbox was the tune!!
So okay, now to the results, the second I started my car I could hear the difference, sounded deeper, then comes the road test, I live in the mountains so I had to take it somewhat easy till I got to a straight enough road to where I could really get on it (I could feel a MAJOR difference in power the second I started driving the car) so I hit a straight road and from about 30 mph I tromped it, car pulled like I have never felt it before, hit second gear, tires spin, not chirped, spun enough that it pulled me sideways a little, pulled awesome thru second, hits third gear, tires chirped, IN THIRD!!!! Car pulled thru 3 and 4th with amazing power, Needless to say, it never did that before this 93 Race tune, so I came to a complete stop and floored it, it smoked the tires off all the way thru first and second gears, I mean all the way, hit 3rd and pulled like a monster.
So, if you want to make the most from your CAI and any other mods you have, I would say definitely get yourself a SCT/SF3 Tuner, you will not be disappointed, and may I recommend if you buy a Tuner from AM/Bama, that you ask for Chris Rose to do your tune, that guy is Amazing!!!!
I cant wait to get my C&L Racer CAI come Friday, Chris told me that adding that to my car with his 93 Race tune is going to be a night and day difference from where it is now, I ask myself, how can it get any better than it is now? (without adding an SC or gears) But, if I believe anyone when it comes to Mustangs, I believe Chris Rose!! So I am very anxious to feel the POWER on Friday after the CAI install and my updated Race tune!
Best of luck to you man!!!!
PS: If you have not dealt with American Muscle yet, you are in for a treat, that company is the BEST company I have done business with, hands down, example.....I ordered my CAI from them at about 12:30pm this afternoon and by 2:00pm this afternoon I had received an email from them with my tracking # which I assume means UPS has my package or at least has knowledge of my package and will have it soon, I have ordered from other companies and it has taken 24 hours or more to receive my tracking #.
AM is on the ball, and when it comes to customer service, they are the most knowledgeable, helpful and professional people to deal with IMO.