This could help you a lot with manual brake sizing.

http://www.jakelatham.com/radical/info/brake_calculators.shtml

Without knowing your piston sizes or the pedal ratio, I don't really know where you'll end up. It really depends on how much stopping force you want for the pedal force, but I am guessing you'd end up with a 7/8" master cylinder.

Using just general rules of thumb, I would start with 1g decel at 100 lb pedal force.

I ran my car with my plan of 6.25:1 aftermarket pedals, the cobra braking system, .45 pad mu, and 100 lb pedal force for 1g decel and ended up with a 3/4 bore master cylinder and about the same pedal travel as my current 11.75" cordoba brake system with a 15/16 master cylinder...which is mostly likable, but the pedal force for a good amount of decel is still quite high.