Testing the fit with ShadowFit
The only way to know a cutout fits is to put the tool in it, and a full shadowbox takes a long time to print. ShadowFit exports a thin piece with the same cutouts as the finished shadowbox, so a shadowbox that takes eight hours to print has a test piece that takes about an hour and fifty minutes.

Reading the test piece
Drop each tool in. If it goes in cleanly and lifts out with one finger, that cutout is done. If it's tight in one spot, measure that spot with your calipers, type in the reading, and use Fix the scale or the extra room Gridbox Pro suggests. If it's loose, do the same the other way. When every tool fits, print the full shadowbox.