I did the larger drum brakes on my 69 428, but used the F-150 parts, almost the same. But, also added larger front discs from an early 60's Ford, so had to use 15" wheels.
My point is that with larger wheel cylinders and calipers, the fluid pressures and surface areas change, so if there is a big enough change on the wheel end, then there needs to be an matching change in the master cylinder. There is a calculation out there to derive the proper needed M/C to match the changed parts. In my 69, I actually found the Master cylinder from a F600 dump truck provided the perfect needed M/C piston size to match the larger components replaced. I also took out the frozen prop valve, and put in a newer one from a Maverick. That combo worked fantastic, and car car stopped very hard and true.
I used the 15" station wagon drums with the big cooling fins. It fit right on.
The proportioning valve I got across the counter and it was not painted black.
At first I ran manual brakes that used a 1-3/16" id diameter master. It worked fine. At a later time after I went back to the 302 I put the power brakes back in. The car didn't like it and I could hardly move the brake pedal.
It currently has a 1-1/16" generic with power brakes, the 67 T/A version of the front discs and a 78 Versalles rear with discs.
In the typical "auto cross" tech inspection test, you can't lock up the rear at all even if you stand on it. It does stop straight and true BUT that there is a little tricky because there are things needed on the springs to prevent diving.
The bottom line, is all the parts are there but even changing tires will change the proportioning set up. The original setup really is for the original tires.
If you mess with those, you need to play with the balancing again so worrying about "the factory" set up is not a waste of time, it's just a start. You give this all to the "pit crew" to work out and you just jump in and drive it.