I have a 1993 mustang GT convertible AOD with 89,000 original miles. The engine is stock, but it has some bolt-ons. It has K&N filter, air silencer delete, Pro-m bullet 75mm mass air calibrated for stock injectors, 65mm throttle body and EGR, smog pump delete, offroad 2.5 inch x-pipes, 2 chamber flowmasters with tailpipes not dumps, ford 9mm ignition wires, msd cap and rotor, and stock 3.27 gears. Axle code E.  Some people told me that I can loose low-end torque if I install the shorty headers. So I need more advice.    

I say go for it, I have never experienced a drop when going 1 5/8 (although with 1 3/4" or bigger you might) especially with yours having some mods.
If you want to save some cash, MAC offers coated or chrome header for less than BBK, but the quality isn't the same.  All I can say is do not buy painted ones, chrome or coated are the only way to go.  

The shorty headers on your 5-liter will work fine. Stepping up to large tubes like 1-3/4 and long tube ones will hurt it. But the BBK shortys will be fine.

Checkout this story online, it is an AOD-equipped 5-liter with some nitrous. We have run a series of stories on that vehicle that start off with the mildest parts. the story online will give you an idea of what combination of parts are needed to achieve similar goals. If I remember correctly, the coupe had shorty headers and ran just fine with them.

http://www.musclemustangfastfords.com/tech/mmfp_0805_penny_pinching_mustang_power_parts/index.html  

Thanks for the info guys. I appreciate it.  

doesn't that car come factory equipped with shorty headers?  

Yea, but they are horribly pinched down on the primaries to make it easier to put the bolts in but it cuts down on their flow.  

^^Agree. I'd just bought a pair of unequal shorty BBK chrome headers for 179 bucks. With handling charges, it is 191 bucks.  Got it from Summit. Great deal!