Re: only running on one cylinder
Coils look good and both plugs have good spark. It only has a single carb but could something in the carb still cause only one cylindar to foul? Also the motor has champion plugs J6C instead of the recommended J4C.
"Tain't the carburetor. As you suggested, a single carb feeding both cylinders can't just feed one. The J6C plugs in itelf won't cause it, but one of those could be bad. Have you tried new ones? Can't hurt to try and that might be the only thing wrong with it. Could also be getting water in one cylinder.
But you haven't convinced me yet that it isn't the ignition system. If not plugs or water, I have to go back there. How good is your "good" spark? Will it jump a 1/4" gap? Are the points clean and in good conditon? Remember, they have to make and break good contact up to around 75 times per second! And how about those spark plug wires? Are you sure they aren't arcing out at certain angles of bend? Have you run a continuity check on them and the coils' secondary windings? Just looking good doesn't get it.
The only oher thing that might cause running on one cylinder is the fuel pump. If the diaphragm is perforated, it will flood one cylinder. But your description doesn't fit that.