I pulled 4 guage from the battery (fused), down the driver side wire tunnel, to a power distribution block under the rear seats. The fuses in the distribution block can be accessed by folding the rear seat bottoms forward. I ran 8 guage to the amplifier and 10 guage to the computer. The computer and amplifier have a common ground, under the front passenger seat. The RCA cables run down the passenger side wire tunnel and are are kept apart from the power cables. Speaker wires run up the center console and into the dash and attach to the factory speaker wires using a store-bought adapter harness. The turn-on wire is the same but running in the opposite direction. USB and VGA cables are also run from the dash and down the passenger side.
There is a (for now unpowered) USB hub I tossed under the center console to help make up the connections to the GPS and Touch screen controller. This will be either moved to the glove box or I'll make some holes in the center storage box which will allow other USB devices (keyboard, mouse, Network, Memory cards, Disks) to be attached, when needed.
At the moment, the LCD is still powered from the ciggarette lighter port. I still need to run a power wire from the PSU up to the screen to eliminate that problem. At the same time I'll run some power for by USB hub. Also the amp turn-on needs to come from the computer, and not the ignition switch. This should eliminate the 'thud' I get when the computer turns-on.
I also plan to tap the gear select lever switch(es) and run that back to the computer. This will allow me to disable certain software features (movies, etc) when the 4runner is in motion.
Right now I'm still working out which software package(s) to run. For GPS, I'm using Street Atlas 2004 and I also have MapPoint 2002. For a front-end and A/V playback I've been trying, MediaCar, MediaEngine, FrodoPlayer, and VOICES. None of them are (yet) the perfect solution, but each has capabilities far in excess of anything off-the-shelf navigation / stereo system. Still, I wish had a ton of time to roll my own code. I'm sure that would be satisfying. On the other hand, if one of these packages would release source code, I'm certain I could find time to code and post bug fixes as well as iron out some of the GPS integration issues. (sorry, I had to toss in my 2 cents on this issue).