I recently finished a Disc brake conversion on a 66 Sport Fury, installed new 73 front disc Brakes and replaced the rear drums. The system includes a new Manual Dual reservoir Master Cylinder (Replaced the old sigle Reservoir MC), all new lines, the adjustable proportioning valve controlling the rear brakes, new wheel Cylinders, new Calipers. The issue I am having is that I am not getting fluid pushed through the system, I can pump the brakes and the MC stays full, but if I remove the lines going to the master cylinder It is pushing fluid out of the ports when I pump the brake pedal, but it does not seem to be distributing the correct amount to the lines. Last night I tried gravity bleeding the system but it still doesnt seem to be dropping the amount of fluid in the MC. Any help or ideas would be appreciated.

Where do you live?

did you "bench bleed" the master cylinder ? If not you need to ... I bet if you disconnect the lines and put your finger over the hole on the MC you will not be getting any pressure ... you need to get all of the air out of the MC piston and passageways in order to push it down the tubes.

First I would blow air through the rest of the system to make sure there are no restrictions. If this checks ok your system is air locked. Open a rear bleeder and hold your finger over it. Have someone pump the pedal SLOWLY ,waiting at the top of each stroke. When pressure builds you will fell it on your finger. Release your finger for a moment and continue. No need to release your finger on every pump. This is much quicker than "hold em down,open and shut the bleeder every time". Also leaving a rear bleeder open 15 minutes or so before you start will help as well. As a line mechanic I've used vacuum bleeders ,pressure bleeder s,etc.
All methods will work, some are quicker.
Doug