1) What do I attach to the isolation transformer? I assume that it would be 2 wires from the 3 Pin Connector on the power supply. I assume that it would be AC Line and AC Neutral, but I'm not sure.
You're right, or you can bypass it entirely if you won't be using the power supply for something else, and hook the iso tranfomer directly to the AC power cord.
2) Do I use the ground (pin 2 on the power supply's 3 pin connector) for anything?
Not for the monitor.
3) Does polarity matter (see question #1)?
One of the reasons for an isolation transformer is so polarity doesn't matter. (without one, you could plug it in backwards and kill the monitor)
4) Is there some kind of an issue with load on the power supply? (I think that the fact is that if I plug in the power supply when the monitor's not attached, that's when I can damage the power supply.) Can I damage the power supply if I only attach a monitor to it?
That tap on the power supply pretty much goes directly to the AC plug, it'll be unloaded if you don't use it for other things (like 5V coin retrun lights).
5) Is there anything else that I'm not realizing that is important?
6) It seems to me like the power supply is just acting as a direct passthrough for the monitor power from the wall socket. It seems like I could just connect the isolation transformer directly to the wall socket, then the transformer to the monitor. Would that work Ok?
I could've saved time if I saw this question earlier.
Yes, that's correct
6) If I didn't use the power supply (see question #5) for the monitor, then I wouldn't be able to use the power supply for other things - like lights and stuff because then I would damage the power supply. Is that correct?
see earlier