I've already thought the computer thing through pretty thoroughly and it parallels with a lot of your ideas.
I am going to put a mini keyboard and touchpad in the armrest forward portion where it flips open.
The IDE drive will be located in the sub gloveback area.
It should all be pretty easy to do...just needs time.
Keep sharing your progress with lots of pics please. I will document my install too.
I don't intend to do a lot of custom software work as it take more effort and time to do things right then I have time for. I'm really looking for good NAV, mp3 playback, and having the capability to do what I need to without being confined to a consumer project. Most importantly, it has to be easy to use and functional without too much tweaking. Just a good audio system and good computing capability in the vacation vehicle to enjoy. I've got my ODB-II, engine management and other interests satisfied in my other car. Plus I've done a lot of hardware/software integration tweaking in my home theater, HTPC, and front projection setup.