I've got the same setup as you, boat and engine.
Did this just start happening out of the blue, or was any maintenance done prior to this and the engine was running fine until something else was worked on?
Getting back to basics, missing on a cylinder is either poor spark or poor fuel/combustion. I'd think spark is the easiest to eliminate. Sounds like you've already isloated a missing cylinder by pulling the plug wire while the engine running, and the idle didn't change. I'd guess if you pull the other plug wires 1 at a time the engine would idle worse. But you might want to check that just to be sure. If it's repeatable and always missing on the same cylinder, then that's sort of a good sign.
Spark testers are pretty cheap at an auto parts store. Or you can make your own with an old spark plug. Check for spark at the missing cylinder and if all seems OK, then CDI and sensors are probably working OK and probably not the problem. If no or random spark, then you're probably going to be looking for an electrical problem. Start simple and check all of the connectors coming from the CDI. The spark plug high voltage is develpoed in the CDI, and there are several engine signals going to the computer to control ignition and develop the HV.
John
