Need Help!!! Intermediate shaft removal

The oil hole in the bottom of the rocker shaft at the 2nd hole from the left has to be large enough to expose enough of the oil hole in the 2nd pedestal from the left on each head) so that is the matter of concern. That oil hole comes up right beside the 2nd from left rocker shaft bolt. (It's obvious if you look.) BUT..... whoever makes the shafts makes the decisions how large that oil hole exposure needs to be. I've seen shafts with the 2nd and 4th holes larger on the bottom that all the rest, and other shafts with all the holes enlarged everywhere (like the pair of brand new MP shafts that I have), and shafts with all the holes smaller (like some PRW's here). So you may or may not find that hole sizing to be any guidance for shaft orientation.

The 8 individual oiling holes for the rockers should be on the bottom. Typically, they closer to straight down, the more like the factory. But I've seen them in various angles. There likely will be a hole towards the inside too, for oil to the pushrod cups.

Got any pix?

PS: Sounds good that you caught the snag in the oil pump... that is certainly suspicious.