After fifty years, a lot of gunk and crud can settle out of the oil, and this stuff can set up like concrete in the sump of the compressor. It could be that fifty years worth of gunk and crud are still in the bottom of the compressor, and your attempts at cleaning it out have only been partially successful. A little blackened oil from this is not necessarily a bad thing if that's the case.
How does the compressor work? Does it build up adequate pressure? Does it overheat? Does it have excessive drag? Any abnormal noises? If it's working okay, put fresh oil in it and run it. If it's not working okay, it's probably time to disassemble it and figure out why.