The MAF is strictly part of the car's air/fuel system, so having an auto trans won't affect it at all. As far as my knowledge goes, the 94-95 Cobras ran with the stock sized 60mm MAF that was factory recalibrated to run with 24lb injectors.
In my humble opinion, I recommend you go with an aftermarket MAF because they have a bigger diameter, which helps a Cold Air Intake system to work better, allowing more air to get to the manifold faster. They are also easier to tweak if you have other mods, or if you want to change your injector size.
My stock MAF blew out a few months after installing a BBK CAI on my 94GT. I replaced it with a C&L 76mm MAF (~$300) and the difference was like night and day. Huge improvement in power and throttle response.
Hope this helps.