I use desktop parts powered by an opus, and they have worked faultlessly.
The m-board is an ultra cheap Microstar K-something with onboard graphics and sound, AMD Sempron 2500+ and a 3.5" 250gb maxtor. The HDD is mounted on it's side, but I haven't used any damping or suspension. The only custom part is the aluminum case, this seems to help keep the temperature down.
16 feet is the recommended maximum for USB cables which should be ample for in car use, but you can daisychain hubs together to increase that.

Best of luck.