This thread is 6 weeks old but I'm adding a few comments from my experience with master cylinder replacement and/or the re-pressurization of hydraulic brake system:
1) SLITS helpfully commented: "Make sure that the push rod is actually in the MC on re-install."
It's also important to remember to re-connect the push rod to the brake pedal before installation of the new MC. Most people never disconnect it in the first place but the Haynes procedure on MC replacement directs disassembly of the cotter pin connection and removal of the push rod from the brake pedal assembly before removing the old MC. Once the new MC is reinstalled, the push rod cannot be reattached. It looks like it should, but there is not enough clearance at the cotter pin connection.
Several people have posted problems with initial pump-up of brake system after MC installation. The most quoted response is to "bench bleed" the MC, but I don't think that is why most people experience that problem. Failure of a hydraulic system to pressurize after its been drained can often be traced to an air leak somewhere in the system. Forgetting to replace the copper washers on the banjo fitting is one example. Another is a leaky caliper.
(AMHIK)
A properly operating brake system should pressure-up after refilling with a few depressions of the brake pedal without having to bleed anything. Bleeding brakes is obviously important, but should not be necessary simply to get fluid into the MC.
My two cents