It feels a little wrong to use the surface plate this way, but it was a clean horizontal surface.
The pistons got scrubbed down with a soft toothbrush in a bath of hot water and dish soap, followed by blowing off with compressed air, and wiping down with ATF.
With the pistons and cylinders clean I went ahead and cleaned the rings, wipe down with IPA, then ATF, them checked the end gap in the cylinder they would stay with for life. Then they went into a sandwich bag marked with the cylinders serial # and the gap measurement.