The commonly done way of rebuilding the M/C back before the days of lawsuit-happy customers and their Great White Shark lawyers was to rebuild the unit with it in place on the frame. There's a BIG nut at the rear of the cylinder where the main brake line attaches that would usually come loose with a couple of licks at one corner from a flat-ended punch and a big hammer, and the piston and a couple of check valves could be changed out. No problem, if the bore wasn't pitted.
I'd reccomend pulling the M/C off the frame, give it a good inspection and hone job, wash it thoroughly with alcohol, and reassemble with a rebuilding kit. Back on the frame, top off with fluid, and bleed the system again. If you leave the pressure line slightly loose as you fill the reservoir, it will gravity-bleed pretty well and minimize the effort of purging the air out of the master cylinder bore.
Jerry
