Hey there, I'm mostly on this board for my Probe, but since I'm into 'stangs as well, I thought I'd check this out and chime in...
I would consider the JBA's...probably only the 1.5" not the 1 5/8" inch shorty headers for your GT. The cobra makes sufficient HP to breathe through the bigger 1 5/8" headers, but if I were you I'd stick to the 1.5" sized ones. Check out www.corral.net
Bob Cosby's '99 Cobra http://www.corral.net/projects/blkcld/
*they had a nice write-up regarding the JBA header install, which will be a major PITA, but well worth it. My 2nd choice would be to install the FRPP shorty headers, with longtubes, you would have to remove the headers to service the clutch/tranny every time, too great a hassle for me....goodluck & regards, PM me for further info or surf around on the modular forum at the Corral-great site :)