You can't just trickle out tiny bits of info. You need to make it easy for the members to help you.
I have had far more than my share of problems with brake systems but mine have revolved around non stock systems.
A basic front disc, rear drum system is not too complicated. You will figure this out.
Manual brakes have fewer moving parts to worry about but often times, you can't get enough pressure to the brakes without some type of assist.
The vacuum booster is the way that Ma Mopar equipped our cars to address the need for assist. Everything from the slant six to the Even the famous HEMI had a mild enough camshaft to run power brakes.
The 440 Magnum had a .450 lift cam and was more than capable of producing enough vacuum to power the booster.
One description that I have used to describe poor braking is this....The force applied to the pedal does not translate to adequate force at the wheels.
To be clearer, you force the brake pedal as hard as you can push but the brakes simply do not adequately stop the car.
I have lived it. I have tried many things but my situation was with a 4 wheel disc system.
For you, it could be as simple as a bad or improperly adjusted booster.
The check valve is only supposed to allow flow toward the engine. This means that suction from the engine draws air from the booster to the engine, thus powering the booster. If there are leaks in the housing or the internal components, you will not have enough "boost".
Someone above mentioned how the brake pedal should drop once you start the engine. This is correct and one good way to determine if your booster is functioning. I recently tried a hydroboost setup in my car and while the manner of boost comes from a different source, the principle is the same. My pedal never dropped and the hydroboost never provided any assist.
As weird as it may seem, it is possible to get 2 bad boosters in a row.
To address a couple of your questions...
No, a proportioning valve isn't the cause.
I suspect that you may have read your specifications wrong. I have never seen a 1.25" master cylinder. You may have read 1.125. 1 1/8" is still pretty large. I run a 15/16" unit in all of my cars. Larger bore master cylinders make for a real hard pedal.