Nope, 94/95 cars used T-5s, those are not compatible. Your best bet is to find a donor car and just swap everything vs buying it piecemeal. Any trans out of a 96-04 will work. The manual trans from your year is a T-45 which can be found on all 96-00 (and a few 01s IIRC).
There is also a WEALTH of information on a dozen+ mustang forums. Use the Google, she knows much... And honestly for the price you'll pay for the 5 spd and all the swap stuff you can find a nice low mileage updated 4R70W, an aftermarket stall converter and do the J-mod and be faster in a straight line than the 5 spd will be.
2000 Mustang GT Steeda #0048 34k miles. 99 Cobra 4V swapped, FTBR IRS swapped, exhaust, tuned by James Gordon.
Just because I give you advice, doesn't mean I know more than you. Its just means I've done more stupid ****.