yeah, that stuff will soften the seals. Hate to say it JP, but you should now seriously consider rebuilding the MC. There's really no other way to clean the stuff out but disassembly and renew the seals. Run a "brake hone" thru the MC on a variable speed drill, slowly using back-and-forth motion with light oil to break the glaze from the I.D. and inspect it for pits and corrosion, too.
Use denatured alcohol as a flushing agent for lines, etc.