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I spent years in R&D, testing and manufacturing as a small engine specialist. I enjoy this type of challenge.
If the one way valve on the bypass is not closing fully you could be getting reverse flow through the bypass circuit.
Is your fuel pressure sensor inline or dead head style?
Have you tried cracking the fitting on the fuel pressure sensor when it is pressurised (preferably without getting a face full of fuel) to see if there is air in the line? If there is, the air being compressible, could give you false fuel pressure readings.
As the pressure sensor is the highest point in the fuel system if I understand your description correctly, any air bubbles could be expected to rise to the pressure sensor.
How are the internal fuel tank pickups connected to the external fuel lines?