There is some science to this, but rule of thumb will probably get you there quicker.
I've been playing around with this at the moment for my Circuit racing car.
Science approach:
Usually you work forwards from calliper piston size and numbers, Disc Diam, wheel diam, Centre of Gravity location/height, weight distribution front to rear, max -G of the stop, Brake pad friction and tyre friction values. This will lead you to a ideal front and rear circuit pressure required.
Then you use your pedal pressure (i.e how much foot force you want on the pedal), pedal ratio and work out the required master cylinder size. Lastly, you need to ensure that the stroke of the master cylinder can move enough fluid for the brake size, so work out the total displacement of fluid required.
Whilst all this ideal stuff is great, when you only have the choice of three master cylinder sizes, what's the point of knowing you master cylinder diameter requirements to 10 decimal places if they aren't available or working backwards to piston sizes that don't exist, rotor diameters that you can't get.
I'm using S4 RX7 callipers on the front of my circuit car (Currently in build), which have a piston Diam of 1.28" and will be using a front Master cylinder Diam of 0.625".
The Key thing I am working on is keeping the same ratio of front to rear brake force. I.e I calculated the ideal pressure requirements front and rear and worked out the front braking %, when choosing the front cylinder based on what is available, I will choose the rear size based on what keeps the same overall front brake %. Therefore I may require more or less pedal pressure to achieve the required circuit pressure but at least I know the front and rear are still in the same %.
If I have miss calculated the max -g and hence the weight distribution front to rear changes, which will lead to an overall change to the front braking %, I can always bias this change out using the bias adjustments on the pedal.
Also, try
http://www.stoptech.com/tech_info/tech_white_papers.shtml for some articles that might help.
Bryan