well, i wouldn't worry too much about the master cylinder swap. i am sure your stock master is a nissin unit, and i know the r1/r6 masters are also nissin. the problem the yzf750 riders had when swapping to the newer four pot calipers is that the stock 750 master is 5/8" in diameter for the stock 6 piston calipers. the r1/r6 uses a 14mm diameter master. since your bike came with four pots as stock, i'll bet the master is 14mm.
not trying to tell you not to do it, just something to check if you didn't want to spend the extra few dollars on the master cylinder. be sure to get some decent pads and some nice braided lines to match your new rotors, though!
Jason, aka: Hooligan
2003 Bonneville T100