I have a 09 scion xb also and I am getting ready to start putting together my mac mini based system. I am planning on getting rid of the stereo completely and going directly into an amp. That would leave a perfect opening for the screen. I don't have any experience with fabrication, but I was going to try molding it in to the dash; probably a 7" Xenarc. The dash piece around the stereo easily pops off and would allow for easy access. I'm planning on using the pac-swi-x to interface with the steering wheel controls.
Why do you need your iPod if you have a mac mini in your dash? I am planning on replacing the iPod connection with a few usb ports.
I don't think I answered your question, but maybe this will help you get some ideas. Let us know what you decide.