I'm not an expert in all of your questions, but I will respond to the ones that I do know about.
When you get the PSU or you can look up the manual on Opus's website it shows you how to wire it. 1 wires goes to ground, 1 wire could go to your distribution block with constant power, then there will a third wire that you can hook up to your accessory line that would also activate you radio, or if you have power that comes out of your radio when its on like for an antenna or cd changer you can use that too and the computer ill turn on and off with the radio. You can also just use a manual switch also.
For the hibernate one - there will be small 2 pin header on the opus that you will connect to your motherboard where the power switch would normally go and when there is a loss off power on the ACC line going into the Opus (ie. when you turn the key off) it will send a shutdown pulse to the motherboard starting the shutdown sequence then after its off it will cut power. You will have to set in window to hibernate if the power button is pressed.
Software is really a matter of opinion... If you like the layout of the program and it does what you want then that good.
My personal opinion of frontend software is RoadRunner. It will do what you want, plus its FREE! Plus everything is customizable and if your not capable of customizing it there are TONS of different skins to choose from. Plus everyone is willing to help you out with questions.
GPS - GlobalSat BU-353 USB GPS Reciever - Easy to install, locks on to Satellites quick, holds a strong signal - even got a signal in my house during testing, and not right next to the window either...5) I would also need a GPS unit and AM/FM tuner for the PC. I have not researched these, but suggestions are welcome.
AM/FM Tuner - Visteon HDZ300 HD Radio Tuner w/ MJS Gadget’s HDR-RS232 cable - great reception, easy setup, works natively in RoadRunner and i think Centrafuse also, since its designed for automotive use its very simple to install in the car. Plus you get all the HD features too
By this do you mean you want to just use the speakers over, or the whole stock stereo system???2) I want to use the car's existing speakers (for the time being).
if you want to use the whole stereo you will either need to find and AUX in for your factory stereo or use an FM Modulator - but sound quality with a modulator will be reduced,
Hope that helps a little bit!