If it was me doing the job, I wouldn't feel confident with the brake bleeding technique you are using since you'r thumb does not provide a good seal, and it gives the brake fluid an opportunity to be contaminated by your natural oils and moisture in your skin. If you have found it to work properly, then keep using it
Andy's link is a good technique, make sure you use a clear length of hose from the bleed nipple to the was brake fluid container. This will let you see if there are any air bubbles or contaminants in the fluid.
A newer (compared to the original NSR) master cylinder I think will always feel better due to less wear and whatnot. I think a radial m/c will again feel so much more responsive compared to a standard m/c.
Just for some more food for thought, I have seen a set of good (4mm thick) rotors with worn brake pads feel terribe....to the point where a real firm squeeze can get the lever millimeters away from the bar.