Welcome to the site. There are a lot of things you can do with a new V6, but correction to an earlier post, there are no aftermarket heads or intakes, only way to make your current heads and intake better is to port match them, put in 1.7 roller rockers (not a lot of gain though), and get a new set of cams (not sure where you can get them for the new SOHC V6s though).
The basic mods like a CAI, tuner, and exhaust will make the car a little more fun to drive, but don't expect to get your socks knocked off. Best mods for you would be to get exhaust first, nothing beats the extra sound, and the torque boost you get with opening up the exhaust. After that upgrade to a limited slip differential and 3.73 gears. This will make the car acellerate better, and will allow for better traction off the line as only your back right tire is currently supplying all the power. After that, it's up to you, but if you're serrious, get a tuner, then get a supercharger and end it.
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Trinity 99 Mustang SVT Cobra 280 rwhp, 290 rwtq
Selena 95 Mustang SVO GT-40 250 rwhp, 275 rwtq (Under Reconstruction)
00 Mustang V6 (sold)
98 Mustang V6 (sold)
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