Welcome to the forums :P
Being the owner of a 2000 mustang, which I have torn apart a hundred times and a big apple fan I feel compelled to help you. You definitely have the right idea about the screen placement. That was something I did a few years ago with an Alpine CVA-1005, that is take it apart mold it into the dash panels and then paint it to match the car, although kind of sucked due to the fact I had to relocate the heater controls, but they fit nicely in the glove box.
Anywho, the 7 inch screen fit quite nicely in the top part of the dash panel. Now I am not positive but I think the small foot print of a mac mini will fit in the lower part of the dash panel. If you are pressed for space, the factory amp (if it is not the mach system) is right behind that piece. I can remember taking it out and thinking I had enough room to build a 10 inch sub into the dash :P.
Also for a USB hub the bezel around the shifter makes a great spot. Just do a little cutting, a lil bondo, and a hell of a lot of sanding, and you got your self a spiffy USEABLE spot for the hub.
As per the power for the mac mini there is a forum post floating around about it. I don’t have the time to dig, but its there.
As per the Amp under the seat… what kind of amp is it. Factory or Aftermarket?
If any of these thoughts are unclear please reply. I am having a hard time thinking coherently lately :P