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Have you duplicated the problem and then checked for spark to see if it was in fact loosing spark, or not?
If it has spark then it has to be dropping the injector. Have you listened to it with a stethoscope to see if it stopped clicking when the problem was happening?
Let me ask you this, how are you making the determination that the #2 cylinder is not firing. What are you doing seeing or touching to make that determination?
I don't want to speculate as there could be one of a million different things going on. Get a timing light as well as a mechanics stethoscope, take the boat out, duplicate the problem. When it's running poorly, hook up the timing light to the #2 coil and see if the timing light flashes or not. If it does flash, listen to the #2 injector and see if it's clicking or not. If your not sure what it should sound like, just listen to the ones that are firing. Let me know what you find.