Common brake fluid (such as over the counter DOT 3 fluid) is hygroscopic, which means it absorbs moisture from the air. This also means any car part made from ferrous metal can rust when it comes in contact with the absorbed moisture. This is why you should flush your brake system evey two years. Bleed the brakes on every wheel, topping off the master cylinder with fresh fluid as you bleed. This helps to remove accumulated moisture.
If the brakes have not been bled in awhile, there may already be corrosion built up in the master cylinder. When you pump the brake pedal to bleed the brakes, you can do damage when the internal hydraulic seals pass over the corroded areas. The best way to check this is to take apart the master cylinder and inspect the bore and replace parts where necessary. If there's corrosion in the cylinder, there probably is degradation throughout the brake system.
Some people pressure bleed by forcing fluid through the system without pumping the brake pedal. This is ok for adding fresh fluid, removing air and moisture, but you still won't be certain of the condition of your brake hydraulics.
Up until 1961, the Stude master cylinder was under the floor on the drivers side. From '61 on it was on the firewall, except in Hawks, where the m-cylinder remained under the floor. The cylinder on trucks didn't go to the firewall until '63.
To remove an under floor cylinder, there are two through bolts that attach it to the frame, which may also hold a bracket for the pedal return spring if the car is a standard transmission. Unhook this spring before unbolting the cylinder. On an automatic trannie, this bracket and spring will be absent.
On the back of the cylinder is a large 3/4" hollow bolt that holds a brass distribution block where the brake lines attach. (Note there are two copper gaskets/washers on either side of the distribution block. These will be replaced with new copper washers.) Remove this bolt - then unbolt the cylinder. There's a push rod from the brake pedal to the master cylinder that's attached with a clevis. Before removing the clevis, take note to which hole on the pedal arm the clevis is attached. Remove the clevis cotter pin, slide the shaft out and then as a unit, pull out the master cylinder. Check the clevis pin for wear and replace if needed.
Master Cylinder Disassembly: Pull back the rubber bellow boot. On some cylinder models the push rod is held in place with a snap ring, which will be removed. If there's not a snap ring holder, the push rod/clevis assembly will slide out with the rubber boot from the end of the cylinder. There's usually a build up of corrosion about 1/4" in from the edge of the cylinder bore. You will need to hand sand this with emery cloth before the piston will slide out.
With the new m-cylinder repair kit in hand, compare the depth of the push rod bore between the old and the new piston. They should be the same. If they aren't, you've got the wrong repair kit. Now remove the cap, if possible. Sometimes these are stuck, corroded on and must be broken away. You may get a new cap from your Stude parts vendor. Hopefully the piston will slide out easily. If not, use a metal punch, inserting it through the outlet hole and gently tap the piston assembly apart.
Congratulations - you now have a parts mess! Grin.
Now that everything is disassembled, clean the bare master cylinder with a solvent product, such as Brake Kleen. Make sure the cleaner is non-pretoleum based, as this will attack the rubber. Brake Kleen is a chlorine based solvent. If it comes in contact with open flame or intense heat, it will convert to phosgene gas, which is poisonous. You do not ever want to come in skin contact with this gas or inhale it... dangerous stuff. It was used as a chemical weapon during WWI.
Inspect the bore of the master cylinder for rust and corrosion. If there are areas of light rust or corrosion with no deep pitting, the cylinder can be honed out. (You may purchase hones from auto parts stores to do this honing.) Reclean after honing. If the cylinder wall pits are deep, rubber parts won't seal and the cylinder must be sleeved or replaced.
Re-assembly: The new check valve seat rubber washer goes in the bore first, then the redisual pressure valve, flat side toward the rubber washer. The piston return spring is inserted next, open spring end first. Then lube the rubber cup piston with new brake fluid. Insert cup end into cylinder with the back flat side facing you. Next insert the aluminum piston with the push rod hole facing the open end. Slide new rubber boot over end of push rod and snap retainer ring into place on the rod, if originally equipped with a push rod retainer. Insert push rod into bore of the piston and install snap ring. Then push lip of boot over the end of the bore.
You are now ready to reinstall the refurbished master cylinder on your car. When hooking up the distribution block, make sure you have replaced (with new), the copper gaskets on either side of the block. Used copper gaskets/washers are compressed, hardened and will not seal properly.
If you want to convert from DOT3 or DOT4, you must flush and clean your brake line system. Without proper flushing, the mixture of 3 or 4 with DOT 5 will damage the seals and cause brake failure.
DOT 5 brake fluid is not compatible with anti-lock brake systems.
To flush your system, fill your master cylinder with rubbing alchohol and bleed pump the brakes until only alcohol flushes through. Using a turkey baster, suck up the alcohol left in the master cylinder. Take all the brake lines loose at both ends and using filtered, dry compressed air blow out all the alcohol. Keep blowing until lines are thoroughly dry. Carefully, gently blow out the master cylinder until completely dry.
Re-attach the brakes lines, fill the rebuilt master cylinder with DOT 5 and pump bleed the lines until all air is pumped out and brake pedal is solidly stopping.