I don't think that is your problem, but it doesn't hurt to check.
What I did was opened up the top of the master and looked into the holes with a flash light.
Loosen the master cylinder and pull it back some on the studs. Then push it back into place and see if the piston moves inside the master when you do that.
If so the rod is too long. They make adustible ones. Or you may just have the wrong master cylinder, as the piston has a hole in it that can be a different depth.