1) Many people use laptop (2.5") hard drives, which are significantly smaller than desktop drives. Laptop cd/dvd drives are also quite popular, which are about 1/2 the size of their desktop bretherin.
2) A mini-itx board really isn't fundamentally different than a normal ATX board. It's mainly just smaller and often have integrated CPUs, though some models have special features. You might check out www.mini-itx.com to get a look at what kind of hardware is out there, and the stuff that crazy people do with them.
3) Check out the Power Supplies forum. The PSU that snap into the MB aren't Opus (I think Ituner makes them?). They are designed to take power from an AC/DC adapter, though you can give it regulated power from the battery instead. The Opus is made for the car, and connects directly to your battery.



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