W98 doesn't require a keyboard to start. You're probably talking about your BIOS giving you errors. Disable error reporting and you should be gravy.
For your startup/shutdown issues, just plug that relay into two pins of your parallel port and (based on your skizzles) write a small program to monitor when the two pins are shorted or not. Power it directly from your battery so that when your car turns off and your voltage drops to ~10V, the relay opens and your computer is told to shutdown. I have some C code to do just that if you're interested.
Unless you're using your head unit to control the volume of your computer, just run a wire from your sound card to your amp.
8 gauge is plenty for powering a PC. I'm using 10 gauge without problem.