Are you sure the master cylinder is actually good? If it's not, it could be simply bypassing, back to the reservoir.
If you get pedal with the rear brake line capped off, but not with it connected, then you probably don't have enough master cylinder travel. Because it's a dual MC, you should have a little bit of pedal (the front brakes should work) when the rear line is not connected or capped.
Slightly drifting from the OP's post, but here's a little info explaining the wet and dry boiling points that are shown on the chart that @mgtstumpy included in post #2. The Dry Boiling Point of brake fluid refers to the boiling temperature of fresh, new brake fluid from an unopened container. Whereas the Wet Boiling Point is defined as the temperature DOT brake fluid will begin to boil after it has absorbed 3.7% water by volume. DOT brake fluid will reach this level of water volume after roughly 2 years of service, which is why it is advisable to renew your brake fluid every 1-2 years. The effects of this water content over time are better illustrated by the graph below. This graph is taken from Shell and gives an overview of the declining effect water content has on its range of DOT 3 and DOT 4 brake fluids. The Department of Transportation specifies the minimum wet boiling point of DOT brake fluids after absorbing only 3.7% water content (roughly 2 years service). In the graph above we can see that the boiling points of the various Shell DOT fluids decline much further over longer periods of time. When brake fluid reaches 8% water content the boiling point of Shell DOT 3 brake fluid has been reduced almost to that of water - 100°C!
I find this interesting, if true. If you are unable to full stroke the master cylinder, it may very well give you some trouble; both bleeding and adequate volume-wise; but more importantly if you ever have a failure of one side of your brake system; you may not have enough master travel to operate the remaining brake system. That couple inches of pedal you cut off may have been a necessary part of the system.
first you might measure how far the master cylinder can travel, then measure how far the pushrod moves when you move the pedal through it's full travel, and see if maybe you need to do something to get more travel at the master cylinder. Although there may be other issues, too.
Here's a cutaway of a Corvette style master cylinder. If you have a leaking internal seal, fluid just goes back into the reservoir. If it is a just a tear in the lip, it will push fluid when the bleeders are open, but will never truly pressurize (e.g. pedal will go to the floor).
I suspect that if you hooked up a brake pressure gauge, you'd find that one of the circuits has very little pressure, and that it falls off almost immediately.
If you if you have even a tiny bit of " preload " or interference when bolting the master cylinder to the booster you will never get proper pedal. You should be able to push the master cylinder up against the booster with 0 resistance from the push rod against the master cylinder piston. If you can't screw the push rod in further put a couple of flat washers between the booster and the cylinder and see if that helps....
Sometimes the calipers need to be down low on the ground so you have to put a spacer the width of the rotor and bleed them down low.