Hadn't thought about running vineger in it. Too late now, its all buttoned up and put away. I did mark it on my calender to do it all again in 6 months just because it was such a mess. I may try that then.
This time around I drained it, flushed it out with a garden hose, refilled it with water and Prestone radiator flush, ran it, flushed out again with the garden hose (still dirty). The water finally started coming out clean in the end but I sure it still got plenty of gunk in it somewhere. It really surprised me given how clean this engine is (without having been cleaned).