wild guess here....assuming the pump is camshaft-operated.........worn camshaft lobe...by swapping the pump, you've eliminated operating-lever, spring, diaphragm, valves......so that leaves the operating part of the engine and the actual pipework......there is an outside chance the fueltank is not venting properly (partial blockage) but i'd expect the tank to "oildrum" * when the boost pump is running as well.
*the "boinging" noise as the tank sides flex in, due to fuel being sucked out and insufficient air getting in to replace it.