OK, I finished up some electrical modifications to the LCD circuitry and got it mounted last night. There is still some clean-up to do but everything works!
I installed my GPS in the factory cubby, behind the screen. It appears to get excellent reception there.
I put the Computer and Power Supply in the passenger side storage bin in the back.
I installed a 4ch amplifier under the passenger seat (blocks the vent a bit).
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 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 harness. The turn-on wire is the same but running in the opposite direction. USB and VGA cables are also run from the dash to the center console.
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 dash 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. 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.
I'll post pictures of the complete install when I get a moment.