I have bled all calipers, starting with the passenger rear, and worked toward the master cylinder. All air is out of lines, no leaks, and brake pads are good. Still have a soft pedal when pressed. Could it be the master cylinder, diaphragm, or vacuum leak?

 

If the engine is running, you will be able to press the pedal all the way to the floor. This is normal. Try it with the engine stopped. Pump several times to use up all the vacuum in the booster. After several pumps the pedal should be very firm.

 

I have never heard it is ok for the brake petal to go to the floor with an engine running, in fact just the opposite.