I have a 1999 Ford Explorer, it runs great then will **** like it is out of gas, then it will stall. when i try turning over it sputters and shakes and never really gets started then stalls again. If it sits there for an hour it will restart but the problem happens again when you drive it a little. I know it has to do with the fuel system just dont know where to start.

It may sound really stupid, but the fuel itself may be the issue... have you put any gasoline conditioners in the tank? Do you typically run with a full tank or empty tank (water condensing in the fuel tank) -- do not forget in the future that the fuel quality sucks these days - small engines, especially 2 cycle are getting eaten up by ethanol and the fuel itself is breaking down rapidly!!
Alternatively, the fuel tank cap may be an issue.Otherwise, the fuel filter, then the fuel pump (test the fuel pressure) - this is pretty much the least to most expensive ways to begin... In all appearances is has to do with the fuel in one way or another...
PS: Good job in putting the problem in writing with details.
Best regards
Ck