nope they won't work. THe reason to this is because the transmission on a 94-95 mustang is a bit longer due to the input shaft. If you tried to stuff some 87-93 long tube headers under a 94-95 car you'll end up having the clutch fork rub up agains the collector. Trust Been there done that.
I had a 94 trans under my 1990 5.0 LX. I tried to run long tubes under my car but, I soon found out that the headers would not allow me to work my clutch at all.