What are the two ports in the 2.0 heads just outboard of the top intake studs on each side? I have a dual carbed car and there are two plugged threaded stud/relief pieces currently installed into each of these points.

Must be late heads. They are part of the emissions system. If you are not going back to the emissions system have them welded up.

They are air injection ports. That hole goes directly into the exhaust port for air to be injected into the exhaust stream via the smog pump.

These engine runs a bit rich. Injecting air (and the oxygen in it) causes the hydrocarbons to keep burning even as they are flung down the exhaust pipe.