Other ideas...
Basically, what you are running into is that it starts fine and after a bit of running it's starved for gas.The reasons for this can be many. Check to make sure your tank air vent is open (Had that happen myself!). The vacuum in the tank wont allow any fuel to be sucked into the engine.Second, check to see if the lines or filter are clogged. The engine is drawing in the gas from the area past the clog and runs fine. When this gas is gone, it can't suck past the stoppage (happened to me on a cycle).Air leak as Tews states, this would cause the fuel to flow back to the tank instead of staying in the line after you pumped it, again starving the engine.Easiest way to tell is to remove the lines and tank completely from the picture and try running it with someone else's tank if you have a friend that can loan you one. Make sure you get ALL the line, including the peices connected to the fuel filter. If you cant find a tank to borrow, you can get a windshield washer or collant overflow bottle and fashion that with some fuel line to be a 'minitank'. Run the engine with just that and see if it does the same thing. If not, then you know the problem is either with the lines or the tank.If this doesn't solve the problem, let me know, I can probably help you out. Old hat to engines, new to sailing!

Personally, in replacing lines, I use a clear braided fuel line. It allows me to see the fuel flowing, or if it's not, and is easier to diagnose problems such as clogs.Josh