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Hello Steve. My name is Tan.
If you leave the engine connected to the remote fuel tank will it run and not stop? If yes then we can eliminate the engine as the problem. Leaving the fuel pick up tube, anti siphon valve or a clogged fuel vent. When you had the pick up tube out did you inspect the tube for holes or cracks? Did you eliminate the anti siphon valve?
Does the engine run on the remote tank without shutting off?
Ok that leaves only one thing the fuel supply line or the pick up tube has picked more debris and is blocked. Can you connect a vacuum gauge in the suction side of the fuel pump?
Oh I can figure it out? We know the engine isn't the problem as it runs on the remote tank eliminating the engine as the problem. So that leaves the boat side fuel system as the problem. If the gauge pulls more than 2" of vacuum you have a restriction or blockage in the system. Have you replaced the fuel line running from the tank to the engine?