Yes it will, but you will need a Fox '93 Cobra specific input shaft and any fox steel throwout bearing retainer.
The thing with Cobra T-5's is they use a revised pocket bearing designed to minimize mainshaft deflection which usually leads to 3rd gear blowing up. The revised bearing requires a unique mainshaft and input shaft. If you had a GT t-5, you could simply swap any old Fox input shaft and bearing retainer on and be done, but because it's a CObra trans, you will need to locate a '93 Cobra spec input shaft. I beleive the T-5Z input is the same.
The Sn95 driveline is a little less than 1" longer than the Fox. Ford compensated by stretching the bellhousing and the input shaft on the trans.