Simple answer here...you're missing the MC
Ford markets the 13" Cobra kit for the 94-95 Mustangs with a master cylinder included in the kit. The GT MC is 1 1/16" bore, while the 94-95 Cobra MC is 15/16"
It was sold as the M-2300-Q kit
http://www.fordracingparts.com/download/instructionsheets/FordInstShtM-2300-Q.pdf
Now, keep in mind this kit was designed with the 38mm cobra calipers found on 94-98 Mustangs. These are mostly replaced by the 99+ 40mm cobra calipers these days. More than likely this is what you have.
Rather than use the 94-95 Cobra MC with the 15/16" bore, a more popular swap (and easier to install) MC used is the 1993 Cobra 1" bore MC.
This is actually the combo I run on my '88. For a short while, i ran a 94-95 Gt 1 1/16" MC and the pedal effort was very hard with a lack of brake response. I swapped to the 1" MC and pedal effort was MUCH better and i could actually stop!
If you do have a set of 94-98 Cobra calipers, you'll need the 94-95 Cobra MC, although you could run the 1" MC. I did speak with a Ford engineer who said the 1994 Cobra originally came with a 1" MC, but Ford changed it last second to make the pedal effort more agreeable for street driving.
1993 Cobra MC will direct swap
94-95 Cobra MC requires brake line adapter kit from max motorsports.
In terms of identifying your calipers....
38mm piston on the left...notice ribbing around the piston bores
40mm piston on the right. Notice no ribbing
Hopefully that helps