Questions:
1) I need the receiver to run extremely silent and cool in a 76-80F ambient environment (plenty of ventilation space). Is the 591 passively cooled and will it run cool? I read that Onkyo tends to overheat.
The 591 is passively cooled. I can't comment on its running temperature, but as long as it has ventilation space then it should be fine.
2) I want to connect my PC to the receiver using optical only for audio (PC will be connected to monitor directly through DVI). Can I tell the receiver to just output the optical audio (with whatever audssey processing the receiver does) OR does it need an HDMI signal also?
You tell your computer to output the sound as optical, then you have the receiver select the input as optical. Audyssey processing is different. It uses the included mic to calibrate your system.
3) I currently have a X-FI and Z-5500 speakers, the X-FI DAC sounds amazing for music and movies, will I notice a difference with this setup?
Probably, but seeing as how I haven't heard that particular Energy system or those logitech speakers, its hard to say how much of an improvement.
4) Does the unit produce any frequency/humming noise?
It shouldn't, unless there's a problem somewhere. I don't think a company would knowingly release a product that produces unwanted noise, especially a home theater component.
5) The receiver will be out of sight, does it include a IR external receiver so I can place it where I want?
No I don't think it comes with an external IR receiver. That is something you would have to get together on your own.
6) What extra wires are needed? I notice on the 591 receiver, there are no "terminal" wires...I don't know what kind of wires are on the Energy speakers but it looks like terminal wires. SO where does it connect?
The red and black things on the back of the receiver are called 5-way binding posts. They accept a varierty of different wire terminations such as banana plugs, spades, and just ordinary speaker wire.