I had a noise from my fuel pump area, too. I'm running a magnum roller in my early block with hughes lifters and fuel pump eccentric adapter, so pretty similar to your setup. I replaced the fan clutch and alternater, before I figured out it was from the pump. Pulled mine and replaced it, which made no difference. In the end, what I found was that the pump arm was rubbing on the timing chain.
No idea why it would show up later, though. Maybe it's a completely different problem.