looks like it is very well planned!
so far, here are the issues that i see with it, you or others might disagree though
the capacitor is useless--it is really not helping anything but lessing the wheight of your wallet. there is a recent thread in the car audio section about that..
for the remote power switch, and reset button, i understand why you want the power switch, but i would highly recommend a reset button also-- i also thought i would never use both, but wired them up because i had the wire(a single cat5 takes care of status led's and buttons..), and have used it more than i would like to admit... for the power button, i am not exactly sure how that is going to work-- most of the dc-dc power supplies have a 'dummy' mode where they just stay on all the time, but can eat up the battery staying in that condition(i think)... most dc-dc's use the switched line to turn off the computer, and go into a 'power saving' mode, where they consume less power until the switched line goes active again.
what about connecting your switch to controlling that remote line on the dc-dc instead? this way, you can have both controls, and the advantage of power saving(with my dsatx, i have left my car sit for weeks, and i don't have to worry about it not starting).
the other issues is the usb hdd. i have not tried it, but i thought there was issues with them, similar to the cf-ide adpater setups. just go with a cheap hard drive, 3.5, 2.5, it really doesn't matter...
1. fuse for the screen-- i beleive that my 629 led screen needs something like a 5 amp fuse-- though a 2-4 amp fuse should also work for a led backlit screen, but definatly never above 10 amps for the screen.
2. like i said above, i think it would be better to remove the cap all together, but it shouldn't matter whether you wire it before or after it..
3. got that one above too.
4. can't speak for the jetta, but overall, most will install it in trunk, or under one of the seats. there usually isn't too much room under the dash--sometimes there is just enough room for a tiny motherboard--unless you remove the radio, which you said wasn't a option right now, and with your current motherboard selection, i have not seen any dash with that much flat, open space...