You can run either transmission, but there are some differences. On the 94-95 transmission, the bellhousing is different, the clutch fork is different, and the imput shaft is 5/8" longer. A 94-95 transmission is obviously the best fit. You can put an earlier Fox body transmission with a Fox body bellhousing, and foxbody clutch fork. The shifter will sit slightly farther forward, and you will have to get a spacer that mounts between the axle flange and the driveshaft. The spacer is not terribly expensive. You can also run a foxbody transmission with an SN bellhousing and clutch fork if you put the SN input shaft in. Changing the input shaft is not very hard to do, and only takes a few minutes. It does not require tearing the transmission apart.
Kurt