Here is my experience with the Aftermarket 62mm Throttle Body, I have dynoed my 2005 Mustang GT with an automatic trans. No other mods other than a K&N Aircharger.
First Run - Stock GT 250 HP
Second - Stock GT w/CAI 263hp
Third - Stock GT w/CAI and TB 269hp
fourth - SCT Tune w/CAI and TB 271hp 280Tq
Fifth - SCT Tune w/CAI Stock TB 272hp 282tq
If you are not planning on tuneing your car to keep from voiding your warranty then you will get better performance and throttle response from the K&N CAI and Throttle Body. The reason why I choose these two products because they advertise no tune required.
After reconnecting the battery and putting the car back on the dyno the third time, the computer was able to compensate for the increased airflow and adjust the Air/fuel so as to not run to lean.
If you plan to tune the car, then I suggest starting with the JLT CAI and Underdrive Pulleys then a Axle-back Exhaust, No HP Gains But they sound Damn Good. With a tune, there are no advantages to the 62mm TB
If you want to get more aggressive, install headers, High Flow Cats or Cat Delete, X-Pipe, then put on Charge Motion Delete Plates and Electric Water Pump. If you are real dareing, Get a little Nitrous Oxide.
If you "Just Say N2O to Nitrous Oxide" Then Go Wild and Get a Supercharger.
This is a little bit out of my league so maybe some one can post the ins and outs of Superchargers.
I've heard once that the computer will adjust to simply a CAI, but mine threw a Check engine light and the dyno showed a drop of about 26 hp and 36 trq(in high altitude also). Anyone who is new at this should buy the Cold air kit along with the tuner.
Make it breathe better.
I did Intake, tuner, longtube headers, and exhaust and picked 30 horsepower, and the car still idle's and runs just like it did from the factory.
I have the CAI and Tuner on my '05 GT. I had it in the shop yesterday and they told me it's not covered under my warranty. What they didn't realize is my buddy owned the car before me and put it on and so when I went to the dealer to buy it, it was covered under my warranty because it was on the car when I bought it. I don't know if it would affect your warranty or not.
I'm not so much worried about that particular part, as much as the warranty for the whole car if something totally intake un-related happens, will the warranty be good... ?
Let's put it this way, if ANYTHING you do to your car... ANYTHING at all... causes a malfunction, breakage, etc. that malfunction or breakage is NOT going to be covered by your warranty; and you're on your own.
Of course, some dealers will overlook somethings... BUT that's dealer specific. Ford HQ will tell you to pound salt.