your best bet is to locate the hardware in the trunk in some specially built box that is
bolted to the car in lots of places. also, to prevent theft, you should have an onboard alarm system (no stickers on the doors so as to keep the element of surprise)
also, you should probably use bolts with non-standard heads (such as resistorx, Torq-set and Tri-wing, which are used in aerospace).
pluging a computer through standard car amps has, in my experience, been virtually painless, just plug straight in, and adjust the maximum volume to your taste (set the computer volume at 75%, and use the control on the amp till it gets too loud, back up a bit, you're set). I recommend using a sound card with RCA connectors, as this avoids the problem of badly designed mini-jacks that eject themselves with vibrations
there is no magnetic problems that I experienced (my car is small and the subwoofer magnets are pretty close from the HDD). Good speakers will have some sort of magnetic shielding.
as for vibrations, it's easy, mount the HDD with the sticker looking to a side of the car. the heads should be able to travel freely in the vertical direction. (ask me if you want to see a picture of my setup)
I recommand using a Via epia motherboard (M10000 - Neremiah is a good choice). You will not need any cooling besides the small fan that is factory mounted (avoids liquid cooling's potential leaks issues).
the easiest way to update the music on the computer is to use a wireless card and access point in the garage. no wires are better than wires
personally, I don't have an FM card, as I don't feel listening to the 20 different channels of clearchannel-broadcasting-like programming...