When installing or replacing a master cylinder, it is critical that all air is removed from the master cylinder. This can easily be done by bench bleeding the master cylinder prior to installation.
1) Place your master cylinder in a vise by the ears (not body). Make sure it is level.
2) Attach a piece of clear plastic hose to the short end of one of the plastic
nozzles. Do the same to the other hose and nozzle.
3) Clip the plastic bridge to the wall and push the ends of the hose through the holes so they are SUBMERGED in the reservoir on either side of the wall.
4) Press the tapered end of the nozzle FIRMLY into the cylinder port hole with a twisting motion. Repeat this procedure on the other port hole.
5) Fill the reservoir with CLEAN brake fluid recommended by the manufacturer.
6) Using full strokes, push the piston in, then release. Do this until ALL the air bubbles have disappeared from the clear plastic hose.
(CAUTION-MASTER CYLINDER WILL NOT BLEED PROPERLY UNLESS HOSES ARE SUBMERGED IN BRAKE FLUID UNTIL THE BLEEDING PROCESS IS COMPLETED.)
Now mount master cylinder and avoid brake fluid leaking out of front and rear ports during installation.
Undo the two nuts that hold it to the booster and put the new master cylinder on. Make sure you use flange wrenchs!!
Don't forget that once the master cylinder is swapped and you attached the hard lines to the new master cylinder, you should still bleed your brakes. Bench bleeding removed the air from the master cylinder, but you still could get some in the lines when you disconnect them from the original master cylinder.
Lastly, you should have a look at how your brake lines are routed (i.e. find how they vary in length). I believe that you are supposed to bleed the longest line first (someone correct me if I've got it backwards)