Could it be bad magnets in the flywheel??
Magnets go south when they get hot, but they usually return when cooled. But since you say you're having problems with both coils (which I agree doesn't make sense)...
I think I'd try putting the coils closer to the flywheel, just be careful they don't crash (bad).
Is there any way you could have a bad ground at the coil?
Did you fully disconnect the mag kill wire? Maybe you have something that's slightly resistive there and it's pulling the coil high voltage down, but not quite enough to kill it.
Just throwin' suggestions at ya...