I also dropped the cylinders and pistons in a bucket full of kerosene to try cleaning them up. A stiff wire brush was able to remove a lot of the gunk, though not all of it so they went back in for a couple of days. I need to see if they are further improved.
Tonight I installed the flywheel and tried checking the lateral runout. I'm fairly sure that I did things right, but unfortunately the runout is about 3x what it should be at 0.012, it should be less than 0.004. I'm going to have to see what can be done about that. Hopefully it does not require removing the crank again, that would rather frustrating having gotten this far. It could well be that I'm reading the gauge wrong.