Well, first may I compliment you on how nice and clean that mag plate is….The only thing I see that may be troublesome is the positioning of those condenser wires…They should be positioned more horizontally on the points so they don’t rub against the flywheel. I don’t think this is the cause right now, you would see the rubbing on the leads, but sure can cause trouble in the future. Looks like the coil primary leads don’t have any insulation on the ring terminals, not that this is a problem, but be sure the leads aren’t inadvertently grounded. You have had this apart so many times, I’m guessing this is not the issue either. Watch out for the positioning of the primary lead as it exits the coil and runs near the crank also…. Are these components OEM? I know you mentioned that the coils are aftermarket, but the points look aftermarket also. I see that you have replaced one of the plug leads, you may as well replace the other one while you have it apart again. I see that you have removed the stop leads from the mag plate, so they are not causing the issue.
How are you checking spark? The spark should be able to jump a 1/4″ gap while cranking, but I am assuming you don’t have one of the conventional spark testers and are just grounding the plugs to check spark.
Finally, the beveled edge of the aluminum threaded mag plate retainer should face down, towards the gearcase. Be sure to use the OMC moly lube in between the retainer and the brass retainer ring, apply a little moly lube to the top of the brass ring where the mag plate rides also. A bit of moly lube should be applied to the brass mag plate bushing also. Proper lubrication is critical here for two reasons….Not enough means premature wear and excessive sideways slop/play. Too much means the excess lube gets into the mag plate and fouls the points….

Jeff, your discussion about one system/cylinder’s components somehow interacting/affecting the other cylinder’s ignition components is very intriguing indeed! Just wish I could understand your theory a little better….
You point out a very important issue though, mag plate slop, no matter what might be causing it, will affect point gap and coil air gap, perhaps to the point of misfiring.
Finally, it is only in recent years when I have gotten into the habit of “reusing/cleaning up old points” on engines used infrequently, that I have noticed excessive rubbing block wear and pay more attention to spring tension. I never paid much attention to these issues in my younger days because I never reused points/condensers.