HELP!!! COOLANT WATERFALL!!

Hmmmm sounds like that 2nd hole goes down into a coolant passage across the back of the manifold but there was not coolant back there previously. Any chance the old manifold gasket was set up to block flow to that back passage in the manifold?

Or, the abnormal repair sequence put stress on the back rear of the manifold and resulted in a cracked manifold back in that area; the crack could have gone from the coolant passage and into the extra hole.

I have serious doubts that you will get the intake and head gaskets sealed right if you don't remove the intake and then start with fresh gaskets. And if the old gasket was not blocking the coolant, then I'd be inspecting that manifold carefully. Sorry....