I'm using a head unit into the factory Rockford Fosgate amplifier. I have an older DEH-P940MP Premier Headunit, using the IP-Bus Aux input cable directly to computer. Extended the Headunit's harness about 5 feet and stuck it under the driverside seat in case I want to control the "amplifer" volume without stopping. But I have it set at about 25% and use the computer for volume control. The sound is CD-Quality, and I'm very happy with it. So happy, in fact I'm selling my amplifier's and aftermarket Infinity Speaker setup (perfect 6.1s and kappa 692.5is running off a RF Punch 4 Channel 500W).
I'm using software as a shutdown controller. It's called ShutControl, Whenever the laptop goes to AC power, it delays about 30 secs and runs whatever programs I need it to, and shuts down. As for startup, I'm running a relay setup for Wake on Lan. So far, it's worked every time. I pulled the WOL diagram from mp3car actually.
As for power... The touchscreen is designed for unregulated use. I've got a couple DC-DC adapters for the laptop (which only pulls 9.5V), and for my HDD/USB (5V 2A). HDD is a 2.5" USB powered hub. It uses two usb ports for 1000ma, but it's working great so far.
I'll look into Allway Sync, but I transfered 3-4gb in like 15 minutes last time I tried it. Which considering the laptop battery lasts for about 3 hours, I think I could transfer whatever I want without any issues. But if I needed to transfer more than that, I think I'll just pull the 2.5" caddy out and take it inside so I don't have to transfer everything twice.