When you are putting everything back together, put some extra time into making sure everything is as clean as possible and that no dust or metal shavings are making their way into the cylinder. Leaving these inside the unit will only cause problems down the line.
Master cylinders are often overlooked, but if you ignore them repeatedly I can guarantee they will sideline you eventually. Some brake problems stem from having worn-out pads or drums, but many problems can be avoided by taking an hour of your time and simply rebuilding the master cylinders.