Hi Andy,
For what it is worth, this is how I have generally started. I have to say it is only the way I have gone about it over the building of a few cars, and it seemed to work out roughly OK, but no promises. A lot will be down to how you like the brakes to feel in weight and travel.
I have always finished up using master cylinders between 0.625" and 0.750". With that knowledge I usually build the car with 0.700" masters frt & rear. I try it at that, using the balance bar to sort the bias. If the pedal weight is OK and the balance bar isnt too biased then great. If the pedal is too heavy, go smaller on the masters, bigger if it is too light. If the bias bar is towards an extreme of adjustment change the master size on frt or rear, making the decision based on wether you are happy to tweak the feel to go lighter or heavier on the pedal pressure.
I'm sure there is a more scientific approach to this, but there are so many variables such as disc dia, radial position of caliper, wheel dia, weight transfer and loads more, my preference is to start with a sensible guess and get out there and see what the result is.
Hope this helps (and makes sense, I often don't!) and best of luck.
Wilt
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Wilt!