What do you want to do with braking system? Do you want dual rotors or just better braking? I've said this here before, if I wanted better braking using mostly stock parts I'd keep the master cylinder, use a high quality Stainless Steel line, use a single GL650 caliper (correct me if I'm wrong on that it's the one Larry uses) ,EBC HH pads, and a cross drilled rotor. Another thing that's virtually never mentioned is the brake lever itself. The modern style give better leverage and feel, however that would require a separate M/C and lever/perch to utilize a modern (sportbike) lever. All these items can be had without breaking the bank. You also can do one item at a time and spread the ebay or salvage yard cost over time. If you want a high tech solution change the entire front end and get better forks as well. Two cents.
Cheers, 50gary