On a 73, if the ignition switch is left on the first notch (notch that would allow the bike to start but not run lights) what is happening that would use battery?

With the ignition switched on, power will be going to the ignition system, so if any sets of points are closed, then power will be draining through the ignition system. The charge warning lamp would also be another potential electrical drain, if it's working.

What about the capasitor? Is there any drain here with the key on opposed to the key being off?

The 2MC is always "ON", as it's connected between the battery and the ignition switch, so the ignition switch position wouldn't matter.

Is the bike discharging while running in this position, or is it simply discharging when left in this position?

It was suggested on another thread that to avoid drain (if the 2MC is causing drain) by the 2MC (little blue can), the earth wire should be disconnected. If this is done, is the 2MC receiving a charge while not earthed and is it again fully functional if the earth is reconnected if ever needed? Or is it best just to do away with the 2MC and connect the wires together while leaving the earth disconnected?

With the (Red) earth/ground wire disconnected, the 2MC would effectively be out of the circuit, so I wouldn't expect it to charge up?
I don't know if a faulty 2MC would be capable of electrical leakage through its casing, but the double terminal serves as a junction for the Brown/Blue wires, so if the Brown/Blue wires at the 2MC are joined together, then the 2MC could be completely removed.