Engine problems

I have a 2007 210 Air Nautique with a pcm engine. I was out last weekend and ran into some problems. The boat started up fine and cruised around for a bit. As soon as I filled the ballast tanks it would not go over 11mph. I opened the engine compartment and found an inch of water at the bottom. I drained it and the ballast tanks. The boat ran fine with no ballast for about two hours. Then it randomly shut off. Started up again just fine and then a half hour later in shut off again. It started shutting off more frequently after that. The oil pressure and engine temp is fine. My first guess is a clog in the fuel line or fuel filter. Almost like the engine was being starved of power. This weekend is suppose to be nice and I want to be on the water. The earliest my mechanic can look at it is this coming Tuesday. Any ideas what the issue might be? Thanks!