2 nuts? All the master cylinders back in that era had 4 mounting studs (manual) or 4 mounting holes (power).
Unless your car has a brake conversion with a newer 2 mounting hole flange master cylinder you need to remove 4 nuts.
I'm sure you have the brake lines off already too. Other than that you should be ready to go, if you have all 4 nuts off, it should come off. It could be rusted to the booster or firewall backing plate in which case a little penetrate oil, and a little banging on it with a mallet or prying should break it loose.