At the back of the manifold where you drilled and tapped it did you weld bungs there to screw fittings into to run the hoses up to the thermostat housing?
I have this mod as well. My intake manifold is threaded 1/2 pipe inline with the coolant port on the heads. I thread the fitting right into the threaded manifold.
I cannot supply those centre freeze plugs. They were custom made by a friend. Sorry.