I just got my new set up...
SVT Header, cat, and flex into a Magnaflow 2.25" exhaust. Man do I love it. I still have a small raspy exhaust leak at the flex pipe which I'll get around to fixing hopefully next week but it's great.
I also hooked up both of my o2 sensors, because I could. Ha! The EGR on the other hand...well...that's to be dealt with later.