The common transmission retrofits are T5's and Tremec's. The reason is these swaps are supported with aftermarket swap kits.
The choices are something like:
a) Windsor-Fox or California Pony Cars approach. Once you select one or other, stick with the engineering approach. Parts don't mix between the two.
b) If you have a 351w then the Tremec is probably the best choice. If 302 then T5-Z (not all T5's qualify).
c) If you race every weekend, then a Toploader 4 speed is probably better for drag racing, or consider a beefed up C4 or C6 automatic.
I'm sure you could put other transmissions in a Mustang. The cost would likely be prohibitive since you'll need a full range of automotive engineering expertise to do it. As you can likely tell, I'm not much of a fan concerning exotic work on Mustang. I feel if you want an exotic car, and have the money for it, a common Mustang will never qualify no matter what you do to it. In this situation, IMHO, I'd be looking for a more upscale car, e.g. Shelby, Pantera, Ferrari, etc.