HI and thank you for your question.
As it sounds like you suspect, the timing should not be affected by water in the bilge (engine area). However, since you mention something that makes you wonder about having the spark plug leads connected to the correct plugs so you have the right firing order, I will address that because it is a good possibility.
The good news is, you only have 2 coils. That means that cylinders 1 and 4 fire together and cylinders 2 and 3 fire together. Typically the spark plug wires are cut to length and often times you can get a good idea of what lead goes to which coil based on that. The closest cylinder to the electric box should have the shortest lead and each successive lead should get progressively longer going to each next cylinder. So cylinders 1 and 4 should have both the shortest and longest leads, and cylinders 2 and three should be the 2 mid length leads. It does not matter which lead goes to 2 and which goes to 3 because they both spark at the same time, every revolution, even though it is on combustion stroke every other revolution. The second spark is just a wasted spark that happens on the exhaust stroke of the 4 stroke cycle. Remember that pistons 1 and 4 are at top dead center at the same time and cylinders 2 and 3 are at bottom dead center. 1&4 and 2&3 as pairs are always 180 degrees opposite of each other. So your firing order is 1, 2, 4, 3.
I would take a close look at the plugs for presence of water on the spark plugs too. Either the engine got water in it, or there is water in the fuel, either of which will prevent the engine from running. To check for water in the plugs, take them out, hold one by the terminal end and sharply tap the tip end on the palm of your other hand to see if water droplets come out of it.
While you are at it, make sure the air filter element has not gotten wet too. If it has, it will need to be replaced.
Let me know what you find and if you need further help, we can go from there.