Changing the master cylinder? You should have had the chance to compare the new to the old.
You may have broken a simple pivot rivet - would place the pedal on the floor - so for the "master cylinder" to be repalced and yet still no action?
Did you verify that the Power vacuum booster and it's chamber was holding vacuum?
There is a regulator air bypass that serves to feed the booster, it also provides a consistent bleed of air past the throttle on top of the EVAP systems own purge line - between the two they provide a means to offer vacuum and a air bypass to get past the throttle plate. Part of the idle speed control it has, with you losing vacuum in the booster, the idle would also have been surging as the losses are pretty high with a lot of air passing the regulator - so that means the booster check valve may have failed.
The Pushrod and it's hardware will have to be checked and inspected - the vacuum booster itself, considering the steps you took to replace the master cylinder - the booster, check valve and it's chamber are certainly suspected - the spring uses the chamber that the vacuum itself works against the vacuum diaphragm - to develop the boost, more than likely the booster is shot as a unit - else if you can fix (replace) the check valve - it may still hold vacuum- without a working check valve - the booster has lost all ability to hold a vacuum.
Best I can do with little I have to work with.