The laser cut panels we designed for the previous (non injection molded) version of the Arduino case have arrived. Similar end plate will be available for the final version so you can get whatever holes you need custom cut to the exact size and shape.
This should give you an idea how much room there will be with a shield installed.
The next version of the text should be more readable. Updated below
Apply ink with a permanent marker over the lettering.
Wipe clean with a paper towel. Use paint thinner if necessary.
That turned out better then I was expecting.
Design your own cutouts for whatever you need, but for now the design requires that plate is ~3mm thick. Ponoko's 3mm thick acrylic is actually 2.9mm thick but should be close enough.
For more information about the design of A Case, check here. Feedback is appreciated.