What kinda clutch linkage are you using??
Some have had good luck with the Hedman 88400, 88406, 88408's though the driver side collector angle can call for creative routing of exhaust by the steering box. Sanderson shorties (can't remember part numbers) appear to have addressed this and I heard they fit better but haven't seen any pics.
Dougs headers for a manual OR auto are supposed to fit with a T5 and cable or hydraulic linkage but in talking to one of their managers that has a Falcon with a T5 and cable clutch...he's using a '94-'95 bell housing that clocks the cable entry lower (about an inch). From pictures I've seen, that does make a difference!
Doug Thorley (I think same or close to Dougs), Crites, and Ford Powertrain make headers for our cars.
I didn't see anything that convinced me a cable setup with '87-'93 'Stang bell wouldnt be a hassle. The cable needs an inch clearance from the header tubes minimum (maybe a little less with ceramic coating), and a STRAIGHT shot into the trans...
I got a deal on a nice set of older Doug Thorley headers and decided to go hydraulic to duck any hassle. If I hadn't I'd give Sanderson a call.