The correct bore depends on what calipers you are using for the disk conversion. The volume of the bore compared to the volume of the calipers will set your pedal throw and the diameter (cross section, really) compared to the level arm on your pedal will set your pedal effort.
Are you going to a power and/or firewall mounted system?
As far as using a tee vs both ports on the proportioning valve, it is whatever you want. The two ports are connected internally so it it is basically just a built in tee. I used both ports on mine because that put all of the hardline joints where they were easy to install and inspect.
