Could be that the pump plunger is sticking in the down position, and the knocking you hear is the cam bumping it instead of the plunger following the cam?, or it is a little sticky, and the knock you are hearing is the pump plunger popping up against the cam. That would be one thing that could cause a knock that comes and goes. It would also explain it coinciding with the oil P comming and going.
Agree with all the above, Slow crank speed = lower dipper velocity and possibly insufficient splash lube to the internals. But if it was a rod knocking, it would start and continue to knock:) Also, not much real oil pressure, it moves the volume, but dosn't make much pressure. I also had to do quite a lot to my 6/1 pump. The pump on the 6/1 I have with the deep sump is actually below the oil level so no real issue priming, but The balls didn't seal, and it took quite a bit to get the seats lapped so it would pull enough suction to move a good volume of oil. If I were contemplating slowing one down that much, I would definitely look into some supplementary oil pump to put oil where it MUST get for long and healthy bearing and ring life. It would also allow for some oil filtration...