It won't be a direct bolt-on. Cobra exhaust is different from GT or V6 exhaust. You can see here 1999-2004 Mustang Catback Exhaust at AmericanMuscle.com - Free Shipping!
that Cobra and GT have different part numbers. Probably due to the IRS.
01 V6 5 spd
Windstar upper, shorty headers, high-flow catted X, American Thunder catback, SCT Tuner, ASP 25% UDP, FRPP T-Lok