The only person that doesn't have a clue is Alien8. What you are saying is "My idea is the only way to go so use it". I myself have been thinking about MP3 car audio well before I found the first car MP3 webpage. One thing that remains the same all along is anytime you use a desktop computer for a car MP3 player you are just creating a hack. Just now are some pretty good looking Car Audio MP3 players starting to be developed that aren't hacks.
If you are making your own car MP3 player then explore your options. Sure using removable harddrive bays is one idea but for me its a no go. I prefer to upload new songs via network connection. With using a harddrive bay I'd have to set jumpers and reconfigure my bios everytime I wanted to add songs. Not my idea of fun.
Getting the audio signal to your headunit is another issue to be delt with. Using a head unit with aux input sounds like a perfect idea. Only one problem. Not many people have this. Another problem is people don't feel like shelling out the green to buy a new headunit. So you have several options such as FM transmitter, Tape adapters, etc. My friend used a tape adapter to go from his cd player to his tape deck and there was no problem at all. For me buying a new headunit is NOT an option. For somebody else it might be an option.
Making your own MP3 Player is all about exploring your options and choosing what you want and can afford.