It's hard to tell what the real problem was since I replaced coils, ignition, and re-checked the carbs (added new main jet O rings) all at the same time.
I should have swapped in just coils first to see if I could forego the new ignition, but you have to take the carbs off to access the wires to install the ignition. And the Dyna looked pretty so I said screw it and installed it. I'm leaning toward the problem being coils since that seems to line up with the inconsistent lean/rich condition on each set of paired cylinders.