In the case of master cylinders bigger is not necessarily better. If you increase the area of the piston in the m/c there will be less movement of the lever for a given applied force when you squeeze the brake. It will therefore probably feel "stronger" but in reality less force is being applied to the brake pads and the stopping distance will increase. See this site, it may explain hydraulics better. It is the second diagram down the page that is relevant.
http://www.grc.nasa.gov/WWW/K-12/WindTunnel/Activities/Pascals_principle.html
So to increase braking power for the same force applied at the lever either reduce m/c piston size or increase caliper piston size or have 2 caliper pistons. This in theory should mean the lever moves further but when I changed from twin single piston calipers to twin double piston calipers I actually found that if anything the lever moved very slightly less, which doesn't sound right but I did change to braided hose at the same time. Another thought was perhaps the pistons in the double piston calipers don't retract as far as the single piston when you release the brake so don't have as far to travel to contact the disk when you apply the brake but that is just my theory.
I actually changed disks and calipers to those off a CB900. Not only do you get more caliper piston area but bigger disks too, up from 240mm to 280mm which is also good. I suspect the single disk machines already have the bigger disk so no room for improvement there.
I'd also recommend using dog leg levers, think they are also called power levers.