I’ve had bad spark plugs do this – try swapping them between the cylinders and see if the problem moves to the other cylinder. You have probably eliminated spark plugs as a cause already, but it’s a quick and easy thing to try.

Take off the inspection cover from the top of the flywheel and check points gaps, and visually look for cracking insulation on the coils. I’ve seen original coils that look pretty bad do intermittent things like this. Like Chris said, when you test for spark as you did, with the spark in free air with no compression, you should get a 1/2 inch spark to insure it runs under all conditions.
Dave

That is a possibility in theory, but I’ve never seen one result with such severe effects. Usually, you don’t even know it is leaking until enough water passes through it to destroy all the bearings in the crankcase.

Agreed, I think the problem is in the ignition system. Did you replace the spark plug wires back when the coils were replaced? The reason I ask is this, some of the auto parts 7 mm plug wire is poorly made, and will chafe after the motor is used awhile. This is caused by the wire rubbing back and forth with the movement of the mag plate. At certain throttle positions, it can cause a cylinder to arc to ground, where the wire is damaged, then correct it’s self after the throttle is advanced. Problem is, they don’t make most spark plug wire as well as the original 50’s stuff. I would take a look at the wires too see if this could be the problem. In short, time to pull the flywheel and have a look. If you are using Sierra ignition points, they are notorious for these kind of problems. I would also check for a worn mag plate bushing…. this will cause the mag plate to be sloppy and move around at idle speed. Keeping a good point gap will be impossible.