"Ok so you say you had the car
"Ok so you say you had the carb rebuilt? Or is it a brand new one? Reason i ask is a carb rebuilt even by a expert has at best a 50/50 chance of ever giving good service. Was the rebuilt carb at the shop that rebuilt it, run on a motor? If not it's not a real carb rebuilt expert doing the work.
The fitting that enters the carb has a filter it clean? There is a filter in the fuel pump, it clean?
Ok you have a fuel / water separator on the boat? Replace the element. Now you know the system is clean, remove the hose from the fuel pump inlet and install a hose that runs to a external tank.
You ever check what psi the fuel pump is giving you? Should be between 4-6 psi no less no more.
Run the boat it fixed, runs good ? If yes then you know it's something with the onboard tank. Remove the fitting that enters the onboard tank, that the fuel hose connects to, it should be a anti-syphon valve. It has a ball in it that allows gas to flow one way, blow thru it, look thru it. It clogged up, dirty clean it or replace it if bad.
The fuel pickup tube should have come up out of the tank when you unscrewed the fitting, it should have a screen on the bottom it clean ?
Next check the vent it clean, blow are thru it, no spiders or animals living in it? If vent is clogged, running the motor will cause a vacuum condition in the tank and the pump can't pump fuel causing the carb to run dry.
Now you have a choice at this point, to pump the garbage and water off the bottom of the tank or not. If you want to, than stick a 3 or 4 foot hose connected to a cheap dc fuel pump that you can buy at any auto store, with a hose long enough to reach a clear plastick container, and pump the garbage and water off the bottom of the tank till you see clear fuel and then shut off pump,pull hose and close up tank.
Long post but the only way to get to the bottom of this problem is to make sure you have a clean system with a good carb."