First off computers for a car are a cool idea. But they pose so many problems that they really aren't practical. First off as you are finding out you have power problems with interference and stuff. Secondly is the whole problem with shutting it down. The best way to get around this is to have your computer running linux and the file system setup with Ext3 or ReiserFS so that if you shut it down without turning the power off you won't do any damage. Also you have to think about the hard drive and the bumps its gonna take. Don't forget to give it a nice cushy ride or you'll be replacing that in no town at all.

All in all the whole idea of a computer in a car is a cool idea, but if all you are gonna do is play mp3s on it then you might as well go out and spend $250 and buy a mp3 deck for your car. It'll work better and look nicer.