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I agree - if the piston and seal was compromised inside the bore, you'd have leakage and rust. After painting, give this area a light shot of Fluid Film just to protect the aluminum and cast iron from corrosion.
For the do-it-yourselfers, replacing seals, pistons, and springs in a master is very easy - it all comes as a kit. (The bore would need examination for pitting, then possibly honing or outright replacement if deep pits.)
How old is it? Has it ever been rebuilt? If it's old or has not been rebuilt in decades, consider rebuilding it. Really easy and the kits are inexpensive. NAPA should have what you need. You have already completed most of the work by having it on the bench. Jerry
Master Cylinder Question
