I went out this morning to do some more trouble shooting. Two things I noticed. The first is no matter how many times I pump the brakes they do not get firm. The second is a whooshing sound while pumping the pedal that never noticed before.
If the brakes do not get hard at all when pumping I would assume you have one of two things wrong.
1) You have a no good replacement master cylinder,
2) You have a massive air leak maybe at the master cylinder.
If at all possible, try to bleed the master cylinder again with a helper. Do not be pumping the master cylinder but instead use full single strokes ie:
Push the pedal as far as it would go and hold it there. Try to let the air out at the master cylinder line then close the line.
Release the pedal, wait a few seconds then push on it again using a single stroke and let the air out again at the master cylinder through the line.
Repeat this process until you are satisfied there is no more air in the master cylinder.
Repeat this process for the combination valve letting the air out at the connecting lines.
If you are satisfied with the results then move on to the wheels.
It is import to use only full single strokes then opening the bleeder and close it before the pedal is released.
Do not release the pedal with a line or bleeder open and do not pump the pedal repeatedly. Air could be drawn back into the system.
If you fail to get the breaks to firm up, replace the master cylinder "again".