Now that my machine is basically working, I’m familiarizing myself with the capabilities and limits of it, as well as learning more about FreeCAD et al. I wanted some way to quickly cad up a test and run it. This is what I ended up with:
(Imagine it with the four screws installed, this was a quick pic, but it has two alignment pins to keep it square 
I milled a 3" hole in my spoilboard to access the bottom, for a vacuum system I already had. The cutout is exactly 3in by 3in. So now I can cut up a bunch of 3x3 squares of various woods, and copy a starting project in cad with a 3x3 stock and all my tools pre-configured. The blanks are big enough to use the Avid touch plate, or I can run a gcode script to re-configure the cnc for that origin.
By combining the vacuum and the 0.1" recess, the blanks should stay in place even with minimal vacuum - at most, with an area that small, vacuum can provide 80 lbs of down force; and yet the cnc has access to most of the blank without clamps or screws getting in the way.
