Also- since your heater line appears to go slightly up from the front of the manifold, did you turn on the heater when filling it? This would help get any air pockets that would sit up in that line after draining your coolant.
Of the coolant you lost: Did you see the coolant on the ground? Where did it go? Due to expansion / contraction, you will see different level from cold-hot-cold. Has the level stayed constant in your expansion tank?
In this situation, there shouldn't be any flow coming out of all the ports if you look down in the radiator tank through the cap. A functioning pump and T -Stat will have antifreeze spurting out a few inches. Wish I would have thought of that before you ripped into it. But luckily it was the problem.