Fellow Scooby Owner! And fellow newbie. Here goes, with little experience:
1. Setup looks good, except the LAN adapter. You are gonna need to have this above any structures in the car, or you're never gonna get any signal.
2. This is gonna take some searching, and some listening. I still haven't settled on an amp, or speakers that I am gonna install permanently. Everybody is gonna give you a suggestion of the amp they have, and its never gonna be the same. Go to your local high end car audio installer, and listen to what they have. If you think you like it, find it online for cheaper!
3. Build a case. Install fans. Don't try to get the air from outside. This sounds like its just asking for trouble with condensation, dust (regardless of vents) bugs, small animals, BigFoot, UFOs, etc.
4. Butt connectors, lots of wire.
5. This is exactly how I have it setup. There are 2 wires running into the back of the radio, yellow, and red. I believe the red is aux wire (on when car is on) and the yellow is constantly on. I may these mixed up. Check 'em with a meter. Lilliput to yellow wire (const on?) and black from lilliput to black wire. Don't forget to wire the filter in the middle (mine came with one.)
6. There has been a post by someone extending IDE to something like 20'. As far as power, Butt connectors, lots of wire.