1985 Ski Nautique fuel problem?

I have a 1985 ski nautique that i have completely restored and has a new jasper crate engine that was put in it just before i bought it. I have been having a problem with the boat quitting on me. It usually fires right up and runs fine for a little while and then will start cutting out and die. It usually want start for a little while but then usually starts back up. At first i thought i had some trash in the gas tank but i took it out and cleaned it well and replaced the fuel filter. I put it back in the water and it ran great for 4 or 5 hours and the done the same thing. Does any one have any suggestions, i am leaning towards the fuel pump going bad but thought that it would just go out and not start working again if it was gone out.

ok thanks, is that a common problem with those boats?

I believe it is although i haven't checked that but u can pour some gas in the carburetor and it would run for a few minutes until the gas ran out. That also wasnt 4 or 5 straight hours.