Hy The Hill Boys, which master cylinder port is used for which system is dependent on whether you are running a disc/drum, drum/drum, or disc/disc system. If you are running a disc/drum system you will need to run the master cylinder outputs through a combination valve, this is to insure that the correct pressures and flows go to the correct systems. In general most master cylinders are plumbed with the primary (closest to the pushrod) operating the front system, but I have seen vehicles plumbed the opposite way. As to the different size ports this was done to make the installation of a replacement master cylinder "idiot proof", so the installer could not plumb the systems opposite to the design. You can purchase adapters to bring the ports to a standard line size, or you could use the nuts which fit the master cylinder ports and are appropriate to the line size you intend to use, hope that helps.
