Hi Dave,
In your first picture, the 2 holes are a manifold vaccum sorce for things like the power brake booster. Use fittings and plugs from the hardware store, the plumbing section. Dont forget to use a sealant or Teflon tape. Try the local speed shop or the old mustang bone yard for the throttle return bracket. 2nd and 3rd pictures, the big opening/hose is for the upper radiator. Lower hose goes to the water pump. Assuming your going with a standard flow and not a reverse flow cooling system. The small hose next to that is the water pump by-pass hose. A small 90 degree hose 5-6 inches long. Get a preformed hose for that one. It connects the manifold to the water pump outlet, the one its right inline with. The hole in the intake manifold at the front that points up must be for the heater core return hose, mine is at the rear of the intake manifold but I didn't see one on the right rear of your manifold. The tempurature gauge sending unit should go into the front of the manifold on the other side of the distributor, intake at the left front. The other outlet on the water pump goes to the heater core inlet, maybe its labeled. I don't think it matters. If you are going to run a heater control valve put it in the inlet hose.
Hope this helps.
PS. Always reference to the right and left of the car as if your in the drivers seat.
Ted.