We are working on replacing the big motherboard with a mini-ITX board, they are pretty cheap these days at ~$100 CAD. Unfortunately using the built-in screen doesn't seem like a good option, it's preferable to be able to use the computer and the MFD at the same time so that instant FE and the GPS map can be used at the same time. The way it interfaces is quite a bit different too, and the built-in display seems rather low resolution, or maybe that's just the software/hardware Toyota uses. The Xenarc LCD screen is capable of 800x480 native resolution, and goes up to 1600x1200 in scaled mode with 2 A/V RCA inputs as well for low-res devices, it came from
http://www.mp3car.com/store/index.php?cPath=25 and same with the 12v power supply.
A Mac-Mini is a great idea, that was my first reaction after seeing it for the first time, but quite a bit more money... However you might be able to mount it in the extra slot so that it's DVD drive is useable. Let us know how it turns out!