I don’t have a diagram that shows which mag is top and which is bottom cylinder. You should be able to visually trace the spark plug wires back to the corresponding magneto. Once you find it, label it directly on the mag!
What bothers me about your motor and also my friend’s motor is that these engines will start and run, albeit poorly, on one cylinder. I have limped home a few times on one cylinder with my 1960 40Hp Johnson. As in the case of my friend’s motor and yours, it should make some attempt to run, pop or produce exhaust smoke on the “good” cylinder. Failing to do that indicates the problem is common to both cylinders. Since the ignition system is separate for each cylinder you have to ask why it will not start (or show some signs of life) on the cylinder with the hotter spark?
Granted you may have one cylinder with a weak spark but lacking any signs of life from the other cylinder is what lead me to the spark plug theory on my friend’s motor. In another post Frank Robb confirmed the J6C is not the same as the J6J. If you have J6Js clean, them gap them and give it a try. If you still lack any signs of life from the good cylinder then look for the common point of failure.
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