Well it's not the fuel pump. I just installed a brand new one and it's still doing it. I checked the drive rod and it has the appropriate spin pattern on both ends and the bevels still match so no wear.
I don't think it's going to be a vent issue either since I had the lines disconnected from the pump and it made the noise instantly as the motor started. If anything it sounds worse. I'm almost going back to my original assesment of a rod bearing. I just can't understand why the stethoscope doesn't pick up any noise from the block.