I just changed my master cylinder tonight, and will run you through some things to hopefully help...
If at all possible pull the master cylinder and bench bleed it. By bench bleed I mean clamp the master cylinder in a vise with the push rod pointing down slightly so the reservoir hose is higher than the output port (with the hose attached to the master, everything including the quick connect on the transmission end), hold the reservoir high and have it full with the cap off, hang the hose down so that all air goes up, push the plunger in until air stops going to the reservoir and the rod is solid (mine moved 1/8" still). Now reinstall the assembly, the pedal might be a little soft at this point, push the pedal to the floor, slip your foot off, repeat like 10 times, this pulls air out of the master cylinder piston. Now crack the bleeder port at the slave with no pedal input.
That's roughly the procedure I used tonight and the pedal feels like new, did the whole thing by myself with minimal cussing, only spilled 1/3 of an adult beverage when letting the jack down...