While driving the boat to the launch, it started, ran fine until almost there. Then the overheat alarm went off and the engine quit. There was water coming out of the port so I think the water pump is OK. It won't crank over until it' cooled down. Now it cranks over but won't start. Checked the fuel supply, fuel filter and plugs. Put new plugs in and checked that I'm getting spark to both. OK there. I've got fuel, air and spark. The only thing I can think of is the timing went off for some reason. Every once in a while it will pop like its trying to start but it only pops once, then I'll keep cranking it and it will pop again but never start. I can see two different timing references on the motor but don't know where to go from there.

Check your Water Seperator is not saturated with water, I would even drain the float bowl(s), and look for the pressence of water.
Try a different fuel supply. (portable tank).
Timing, usually doesn't usually go out.
If you like this Motor, I would invest in the Service Manual.
Good Luck

You must be thinking of another motor as this one has portable tanks. It's a 2-cyl. 40 hp Mercury outboard motor used on a pontoon. It only has one carb and there isn't a water separator on it. I did changed the gas-oil mix fuel and drained the carb bowl with the same results. It will spit once in a great while when I'm cranking it over but that's it.

Do you have any info on how to at least check the timing? If I don't have the tools, I have access to them.

Thanks

Some small boats also have internal tanks.
I can't help with the timing.
I would add a Fuel Seperator.
After you drained carbs, and got a fresh tank of fuel, Did you pump the bulb to flush the lines, before attaching line back to Carb?