My fiancee also has a 99 V6. There are several things you can do to upgrade the power in your Stang.
Dual Exhaust Conversion - This will definitely help, but not 15-20 HP that they claim. That number is achieved on a highly modded motor as compared to the stock system. Expect 5-10 HP from this.
Underdrive Pullies - This is a good bang for the buck upgrade. I have not seen kits for the V6 cars, but I am sure they are out there. The V6 martket is growing tremendously. Expect 5-10 HP from this.
K&N/Remove Silencer - This is a common upgrade. More air in means more HP. Try one of the cold air kits by Moroso, Mac, or BBK. These give the most gains. My Moroso kit gave me 8 HP. Expect 5-10 from this.
Blower - A blower (supercharger) is always worth some big gains. They do make kits for the V6 cars, but they are rather pricey. Downs Ford has a section solely dedicated to V6 power. Steeda also offers packages. Expect 30%-50% power gains depending on amount of boost.
Gears - Never underestimate the power of gears. It does not give you HP, but it sure makes you ride quicker. I gained about 3 tenths by installing my gears.
The last 2 upgrades require a custome burned computer chip I believe, someone correct me if I am wrong. I am considering several of these upgrades for my finacee's Stang. Sorry so long! I hope this helps!
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91 GT, Built AOD, Art Carr 2400 stall non-lockup converter, solid input shaft, Transgo Shift Kit, Tranny cooler, Moroso Cold Air, Pacesetter off-road H, BBK alum. underdrive pulleys, 2.5" 2-C Flows, 13* timing, 3.73's, for now...
MY 91 GT