I'm pretty sure it's the module that controls the one-touch down function on the driver window. I know the driver window won't work if it's unplugged, not sure about the passenger.
I don't think that's for the windows. I've pulled apart some 94-98 Mustangs that do not have that. It might be keyless entry/theft box, to go along with the ones in the drive side of the trunk. That's just a guess though, because all Mustangs have the one touch window.