I wonder if the folks at Arduino have put those doted lines on perpose. If they did, they should put some more. Title circles would be nice (for those screws and distance holders). And lines at the other side for SD input.
I have used the smaller Really Useful Boxes (from Staples, Office Max) for putting stuff in. The clear plastic is easy to drill holes in or cut out openings.
I drill a series of small holes and finish the opening with a box cutter, or use a Unibit type of drill.
Nice work... That I call recycle... I notice in the last picture, a box with a lots of leds ? Some kind of led's matrix ? That look an interesting way to place them into a small cardboard box.
It's small saving The part is only a dollar or two when it's not free. When I ordered 180mm*180mm jobs on ponoko, shipping is $10 and parts+work is another $10 for acrylic.