Because the topic of exhaust is such a subjective matter, you'll get a plethora of responses. To help you out, ask yourself a few questions:
"What (exhaust) sound do I like best?"
"Straight through or chambered style?"
After you answer those, you can choose accordingly. A good resource for Mustang specific exhaust info is
www.mustangexhaust.com . Better yet, listen to a few different exhaust combos in person to get a better feel for what your ears like.
Personally, I'm a fan of straight-through style muffler designs (ie - Magnaflow, Bassani, Dynomax, et al). To each his/her own.
FWIW - 03/04 owners are freeing up LOTS of power by uncorking the very restrictive factory H-pipe and catback on their vehicles. I'd start there first.
As far as headers go, I haven't seen an overwhelming number of 03/04 owners replace the factory exhaust manifolds but I could be wrong about that.

I think a lot of people are still hesitant to install headers on their own because of the amount of work involved. If you do get rid of the factory exhaust manifolds, get longtubes (pending any emissions testing in your home state?

).
G'luck.
