Worked a bit today, seems like good news. I removed the cylinder and piston and measured, sure enough piston skirt to cylinder "skirt" allows the 0.003" and the 0.004" being very snug, 0.005" would not fit. This makes me feel a bit better about the cylinders and I am keeping my fingers crossed the replacement rings will solve my large ring end gap.
Not sure if it matters at all, 3rd picture is the 0.009 feeler inserted between the cylinder wall and the piston wall, not the skirt. Essentially 90 degrees away from the skirt measurement.