I've never seen anyone drill 2 holes in the block before except to drill steam relief holes, but all the original 400 blocks are over 30 yrs. old. I have seen people drill the block and then drill 1/8" hole between the simese cylinders just below the deck to relieve the steam after plugging the steam holes on top of the deck, then plug the outside block holes, this may be what you have. As to using the block holes to transfer the water, i don't see how that would help cool the heads which is the purpose of the top water exits. I think if i were to do it i'd turn the manifold upside down and drill the the coolant hole from the manifold mounting surface, then use a spot facing tool to get a flat suface on top to put the 3/8" pipe thread into the manifold, all you need is 4 or 5 good threads to seal it. It doesn't matter if the holes are drilled on an angle as long as the fittings clear distributor and the carb mounting base. I think you would need a good drill press or better yet a bridgeport milling machine and be able to clamp the manifold solid before drilling or spot facing the top of the holes. Fortunately i have that equipment available to use.
Zip.