Just some thoughts:
When you replaced the coil under the flywheel, Did you by chance remove the metal frame it is on? You may now have too much air gap between the coil and the magnet. It should be something like .010-.012. Problem is, the old procedure was to use a cut-away flywheel to check it.
Another thought is to check the insulation and routing of the high-voltage lead to the spark plug.
Another thought is to operate the engine with the points cover removed. There should be only a minimal spark between the points. Lots of blue sparks there means the condenser is not doing its job.
It is not unheard of to get a bad new coil or or condenser.
You did replace the spark plug, Didn't you?