This is a really interesting thread for guys like me, because it is so well written and descriptive. Lots of good stuff to learn about.
It is really presumptious of me, a wrencherwannabee, to suggest things to you Smitty. But in the unlikely event that you haven't already checked these out, here are some things that I would try:
1 Try brake application with engine on and off. You might be able to learn something from the feel of the booster. (I have learned the feel of no-vacuum boost on the brakes when I have problems with the idle circuit of the Carter. Not a recommended procedure!) You will get a good idea of the pedal travel/pressure ratio with and without boost.
2 Make sure that you are not pushing the master piston through the primary circuit into the secondary. That will, I think, give you excess master piston travel and consequent excess pedal travel. None of your brake lines are crossed from primary to secondary or vice versa, eh? (Actually, I don't even really know where and if they can! Maybe at that little ball valve signalling that you are on secondary?)
3 While she is still here you might want to put your daughter to work for 5 minutes applying the brake pedal while you go around the car with the wheels off to see what sort of brake pressure you have on each wheel. She should be able to feel, on the pedal, you pushing and prodding on the wheel cylinders or the calipers.... Especially if you have the vacuum off. That might give you an indication of where the problem is located.
The above are pretty obvious, but you never know.
In any event we are all waiting to find out what is causing this mysterious delay to the roadworthiness of the money pit!