I had a similar problem to you where the system would reboot for no apparent reason and sometimes would hang at the windows boot screen. It would then go into and endless loop or reboots. I didn't investigate too far before I pulled the pc back out of the car.
The things I would look at is are you overloading the different voltage rails. What m/b and processor are you using? Are you running your screen off the opus? What else are you running of the psu? I think that my problem was related to my alternator playing up and dropping the supply voltage below the low voltage shutdown point.
If you do find a solution, please post it. I would like to know what the problem is.