> If using S13 front brakes and R31 rears (or similar), I will need a 13/16 or 7/8 size master cylinder.

No, you can use the stock 11/16" size.


> What are the differences between 7/8 and 13/16?

1/16 inch. Larger diameter requires more foot pressure to stop the same. But in return there is less travel. The smaller master will stop better for the same leg pressure, but the pedal will move a bit farther.