If there is a problem with the power booster for the brakes you should have issues with idle when you are braking.
Most engines do not like having that large of a vacuum leak and will begin to idle poorly or die when there is a problem with the booster. Usually a sign of the booster going out is the brakes are harder to push, as there is less assistance from the booster.
I found the easiest way to bleed the brakes on my car is with it running, this way the ABS pump has power and is functioning while you are bleeding it, you said you replaced your master cylinder. If a master cylinder is not bench bled properly prior to installing it, there will be a lot of air forced through the entire system making it soft.