Hey, hwood, I finally got around to measuring. There's not enough thread length on the screws to use a 1/4" spacer.
The spacers you have can be filed/sanded/cut down no problem. However, there are some changes I would suggest:
1) Change the spacers and screws. The spacers won't fit in the holes in the corner of the acrylic piece right now anyway. Do you know what size those holes are? I don't have calipers here. I recommend some basic stainless or black oxide button head screws with a steel threaded spacer. Would probably then fit in the holes in the acrylic mid layer (steel standoffs tend to not be as thick as the plastic ones). Like some of the black oxide screws here:
http://www.mcmaster.com/#socket-head-cap-screws/=3hchc6npmailiq27di and here are some threaded standoffs:
http://www.mcmaster.com/#threaded-tubes/=3hchc6npmailiq33rc2) Make the screw holes in the plate much smaller. They are pretty big right now. If anyone wanted to use smaller screws the head might fall through or show some of the hole if misaligned. IMHO there's not any reason for the huge holes. They force you to use larger diameter screws, which force you to use a larger standoff, which is part of the above issue.
3) I like the idea of having a hole in the spacer layer for the usb port, rather than the break as it is now. That will help hold it in place better. If you don't end up doing that, however, I do think having shorter threaded standoffs will allow the top and bottom plates to squeeze the acrylic properly and prevent slippage. Especially if you have proper threaded standoffs in the corners.