Engine gone from bad to worse

[scootc]

Hopefully someone can help me with this.
Over Memorial weekend, we got caught in a storm and managed to get hit by a few freak waves. We took on a lot of water and wound up with just about everything in the boat soaking wet. As we struggled to get back to the ramp, the boat started losing power - meaning I couldn't seem to get the engine to run up like it should. We pulled it out, dried everything off and changed the fluids.
This weekend, when we first launched the boat it ran great for about 10 minutes. As I was idling back to the dock to pick someone up, it began to run rough. Then it would hardly idle. Then it would only run above 1200rpm. Pretty soon I could barely keep it running. Eventually it quit altogether. I haven't gotten it to start since.
I know what you're thinking, and yes, I drained some gas out to see if it had water in it (about 5 gallons). It was clean. I also drained the fuel water seperator. When I crank the engine, I can get gas to spray out the valve on the fuel rail. I'm also getting spark at each plug.

At this point, the only thing I can think of is there is some computer that's not telling the fuel injectors to open. If it is, what computer? Does anyone have any other ideas?

Thanks for reading.

[Tip]

What engine do you have? It sounds like your fuel pump is working fine and if you don't have water in the gas then the ECU sounds like a possibility.
However, the fact that your boat ran fine for about 10 minutes makes me suspect the fuel. How did you drain the 5 gallons of fuel? Unless you siphon the fuel from the very bottom of the tank you won't know if there is water in the tank.

Tip

[scootc]

I have an '01 2300v with the 315hp 350mag.
When I drained the gas, I broke the line at the water seperator and ran it out to a pump and a bucket. I figured this would be the best way since it's where the engine draws it. I even took several samples with the front jacked way up and again with it all the way down.
I spoke to the service manager at our dealer today (thanks Kevin!), and he thinks it might be the ignition module in the distributor cap. This is a lot cheaper then an ECM ($50 versus $1,200) so I'll try it first.