defiantly the duel exhaust.. speaking from experience dude you def want to get a magnaflow there the best... i have a v8 stang and i just put on a duel exhaust and it just makes the car sound and run better. Also if you got some extra cash getting some new headers while your doing the exhaust is not a bad idea. but the guy above me is right. the cheapest and most effective things you can do to get air into the engine are to get a cold air intake and if your feeling good i would suggest a 75mm throttle body and big lube tube it adds 18-20 horses and makes the exhaust sound that much better.
Dual 2.25" pipes were OEM on the GT Mustang, so a single 3 inch would be fine on your V-6. However, the problem with 3 inch exhaust is getting it bend over the axle without crushing it. Dual 2.5" pipes would definitely take away bottom end from your ride.
Short answer, one large pipe will flow as much as two smaller pipes.
The first rule of making horsepower is getting the most air in and out of the engine. Go with the dual and you are on you way to solving half of the equation. ( just don't forget about the getting the air in part )