Which master cylinder bore size to use for power disc Kelsey/Hayes

Step on the pedal;
If it is not high and hard right away; Something is wrong
Give it three rapid strokes and immediately keep the pedal down; If it is now high and hard; then something is not adjusted right. Could be the rear shoes, but could also be that the front pads are not properly fitted.
But if it never gets hard then; one of four things is wrong;
1) there is air in the system, or
2) the front hoses are expanding, or
3) the M/C is leaking internally, or
4) the pushrod is not adjusted properly
All of these are simple to find and simple to correct.

I have those KH stoppers,
with braided hoses, and the standard 10x 2 rear shoes with 15/16 W/Cs, and a 15/16 M/C with a Booster off a mid 70s F-body; All parts were used when I got them, and rebuilt by me.
I run 295/50-15s on the back and 235/60-14s on the front with NO PROPORTIONING of any kind and without exception, these are the best A-body brakes that in 54 years of driving almost exclusively As and Fs, I have ever had.
What I'm saying is; Keep after it;
the parts and the combination thereof, are more than adequate for a street car. Randomly changing parts may cure the problem, or it may not.
BTW
Make sure your front wheel-bearings are adjusted accurately. Because on these brakes the caliper is fixed, as the rotor turns, it knocks the pistons back into their bores. This creates the clearance that prevents the pads from dragging, a good thing. But if the bearings are loose or the rotors are warped, the pistons may get knocked back too far, and the next time you step on the pedal, they come late to the party if at all.
Contrary to the factory literature, these rotors can be machined on modern brake lathes.