Have you checked the distributor cap for cracks or moisture?
Is it carb or FI? If carb, when is last time you had carb rebuilt? Check the fuel filter screen going into the carb.
Have you checked resistance of spark plug wires? An easy check is to run a screwdriver down the length of each wire with about a half inch spacing. If you see sparks jump to the screwdriver then you need new wires. I can look up the resistance specs if you want to check them with a multimeter.
Pour contents of fuel/water separator in a jar to see if you're getting water in the fuel. Let it set for a while after pouring it in to give it time to separate.
Take a look at the spark plugs. See if anything looks off like wet tips or sooty.
Any chance you have a clogged exhaust?
Any odd noises or smells?
2006 Bayliner BR205
A1 Gen 2 1.47
5.0 carb engine