When you bench bleed the new master cylinder, do NOT use the full stroke, just pump the first 1/2" of the stroke. The master cylinders made today can damage the seal at the far end of the stroke. After you mount and connect the master cylinder, use slow short strokes to build up pressure in the wheel cylinder before opening the bleeder screw. Try to prevent the pedal going all of the way to the floor and use slow stroke movement both ways when bleeding.
After bleeding all 4 wheels, adjust the push rod by moving the pedal with your hand and listening for the click when the push rod touches the master cylinder piston. Adjust for 1/4" - 1/2" movement of the pedal before the push rod contacts the piston. I like to stay near the 1/2" limit until I have driven the car for a while. Brake fluid expands when it heats up and the longer space, allows me to determine if the fluid is getting hot enough to raise the pedal.