First of all pwm control can and does, if properly operated , will actually be able to make a pump run at higher voltages than battery power.
Now, my curiosity gets me, IF your pump is external and after it runs for a time the pump starts making noise, it actually sounds like it may be overheating and the clearances opened up causing it to cavitate.
Too ask some specific questions.
1) is it ran from a relay, if so how heavy of wiring on the load side and are all connections solidly crimped AND soldered?also is relay power directly from battery
2) is the pump grounded to the frame, body structure, or separate ground?
3)How are the lines connected to and from the pump, compression, AN, Inverted flare, other.
A fuel pump MUST be relayed and have heavy connections to perform properly.
Just some ideas.