Help Master Cylinder Puking

I hope the new MC came with a new rubber bushing to put on the end of your brake rod to secure in in the MC piston. If not, it might be possible for the rod to come out so you can't brake. I don't know if the pedal can pull it back far enough for that. Looks like you have a power brake MC you are using for manual brakes. Manual MC's should have a dust-bellow bolted to them, which also secures the piston in the bore as those keepers did. Most manual MC's come with the rod and bellows installed (check rockauto photos).

I always bleed the MC in-car, using the brake pedal. You might need 50 strokes to sweep all the air bubbles out. Also would have been easier to pop out the brake rod while the old MC was in-car, using the brake pedal as a lever. Remove the brake switch first so you don't bang it. That switch always needs adjusting afterwards. It should sense pedal motion but not affect it, i.e. pedal shouldn't bottom-out on the switch.