I don't generally give advice, usually just come to read and look at hotrod builds. This problem seems familiar though. If the boat sat up any period of time with old fuel in it(even if you added fresh fuel) the old crap gas in the lines and bottom of the tank will varnish the spark plugs when you first run it. When you shut it down the first time the bad gas will bake onto the plugs in the form of varnish, which is an insulator. No ignition system will fire through it. Now that you've likely ran most of the bad gas through it, put a fresh set of plugs in it.
I also had a 454 mercruiser with a weird random misfire one time. Everything was new on it and I discovered the new rotor cap center blade where it contacts the distributor cap button looked flattened out. I carefully bent it up some to make sure it was firmly contacting the button and the random misfire was cured.