The 5 speeds that will fit your car exactly will come from any 87-93 2.3L Mustang (T5 transmission). The T5 out of a 5.0L car has a larger input shaft and will not fit unless modified. The T5 out of an 84-86 SVO or 83-84 Turbo GT or Capri RS Turbo will work, but good luck ever stumbling across one of those. They are also the "non-world class" type T5's and are somewhat weaker. I am unsure if a T5 out of a turboTbird would work, but I don't see why it wouldn't. The 87-88 ones did have a hydraulic clutch setup though and the trans-crossmember mount may differ as well, but that I am unsure of. You should be able to find an 87-93 2.3L Mustang T5 fairly easily.
The T5 out of ANY turbo car will have a different speedo gear than yours does, so you would have to change it out.
'87-88 Turbo Coupe T5's are identical to any others except for the speedo gear issue, and they have an electronic speedo drive as opposed to the cable drive on Mustangs, so you'd have to find one of those as well.