I would star by replacing all of the rubber hoses from the fuel tank to the fiters, transfer pump, and fuel cooler. These have been known to get small cracks or pinholes and allow air to get in the fuel lines. The transfer pump can be going bad also. If you install the upgraded new one, it absolutely needs to have fuel lines rerouted correctly or the pump will over-pressurize the injection pump and will make it run rough and can damage the injection pump.
