I experienced exactly what you did based off your description a few years ago on my Z1000. Randomly under throttle it would run like crap. I would kill the throttle switch while pulling in the clutch then would pop the clutch to restart while cruising. This would clear the poor running and misfiring for a little while. This continued on through a whole tank of gas. Once I dealt with this for 140 miles and refilled, problem never ever reappeared. Coils typically work or they don't. If you have a crack in the coil case or insulation issue on the spark plug wires, you should only be experiencing these symptoms in the rain. I have had my share of ignition related issues on older multiple cylinder Hondas and from this experience, it is very difficult to run with two dead cylinders if it could at all. In the automotive world, the most common failure of catalytic converters is due to misfires. The raw fuel melts the honeycomb catalyst. This is normally related to failed coil packs or clogged Egr ports. Curious to see if it reoccurs. Even the best gas stations have issues with contamination in the tanks. Especially when they make the switch to winter fuel and vice versa. Most common time for us to get random misfire codes.