Not sure where the noise could be coming from or why. I can tell you that I don't think it's the 2 different parts. I have a Saginaw pump which is basically GM and it's hooked to a Ford MS2 R&P with no problems.
The problem I ran into was pump pressure. My original Saginaw pump was rated at 800 PSI................the MS2 R&P needed a 1200 PSI pump.
That may be the problem with your setup...........pump pressure.