Went through a similar process with an '80s 9.9. Went from no spark on one of the cylinders (turned out to be a dead magnet), to weak spark on that cylinder. Replaced the sensor and the drive coil, and spark was restored.
That's the short story. Either through some testing or switching out parts, I ruled out the coils, power pack and stator (and discovered the magnet issue, which I hadn't run into before). My symptoms sound similar to yours on the problem cylinder. When I had spark, it bridged the 7/16 gap, but weak -- single spark, pale color. The other cylinder output was clearly sharper and brighter.
So based on that experience, I'll suggest it could be either the charge coil or sensor (or both, as I just replaced both out of frustration). If you have replacements in hand, you might try switching one or both.