I finally got some time off of work to take my car apart, measure my dashboard and do some more planning. Just as a re-cap, my plans are to install a lilliput motorized monitor inside my HVAC openning and move the HVAC controls and a mac mini into the lower 2 DIN stereo slot. The area on the bottom I will probably design a dock for an ipod and my cellphone.
The HVAC openning is 9" wide on the inside of the openning and 7.75" on the outside of the openning and 2.5" tall. The Stereo openning is 9" wide on the inside of the openning, 7.75" on the outside of the openning and 4.5" tall.
The monitor itself fits very comfortably inside the HVAC openning even with the accompanying sleeve. The stereo is 7.25" wide and 2" tall. With the sleeve, it is 7.75" wide and 2.25" tall.

You may have noticed in the earlier pictures that there is a large metal bar in the HVAC openning. It appears that there is still some clearance behind the stereo and between the bar. I'm thinking of somehow attaching the stereo to the bracket on the sides for support.
The positioning of the screen inside the HVAC openning works out better then I thought it would. The image is from the driver's perspective.
This shows the very minimal clearance I have between the screen and the dashboard. I'm a little concerned that in order for the screen to work properly it will have to stick out of the dash very far. I just don't want the stereo to stick out so far that it has a giant "steal me" sticker on it.
This picture is looking down through the HVAC openning. I am a little concerned with putting the stereo in the HVAC openning because of its weight. There is no support underneath the openning and the HVAC controls are only supported by the 4 screws in the front. There are two support brackets inside the dash that the stereo bolts into and I was thinking of welding a bar accross the top of the brackets to support the bottom of the stereo. Looking at it again, it would be much easier to use industrial strength zip ties and affix a piece of fiberglass to the top of the brackets. I'm not sure what I'm going to do yet. A friend at work has promised to help me.
I'll let you all know when I have decided on a design. All suggestions are welcome. Thanks.
-Ross