I think I posted this link on this board in another forum. I don't know who the originators of the idea were, but they had a great idea!
http://weldingweb.com/showthread.php?t=97071 post by COO
Trust me, this way is 100,000x better than any other way I've seen it done. It's foam, form-fitting, AND CLOTH COVERED! I used smooth-on.com stuff for the foam, much better than insulation foam.
Cut little 1" disks out of plywood or what ever using a holesaw, and cut them in half. Or slice a dowel rod into disks then half the disks.
Place them next to the tools when you put them down for the finger holes!
Forgot to add instant edit:
I'm about to remake mine. I thought of an idea after I did mine, and it's been bugging me since then. To make it EASY color-contrasted instead of having to individually paint each hole is super easy with smooth-on stuff. Do a thin layer of silicone or rubber on the top layer, then cover it with the foam colored differently.
You could use a flexible urethane 6x foam urethane, and for the top layer that would get abused from constantly reaching in to remove the tools etc use a flexible medium-shore hardness abrasive and chemical resistant top layer!
I'm definitely going to go this route when I redo my boxes. That website is a literal black-hole, much like tv-tropes. They have hundreds of how-to's with tons of pictures and a bunch of videos. After spending a few sleepless nights on that site, I have so many ideas of stuff to do around the shop. I have their plastic casting kit coming in.
It's a kit that lets you make a mold of part(s) and then make copies of it in much stronger plastic, or any material really. I work on quite a bit of old cars and it's very hard to neigh impossible to find uncracked/unblemished plastic parts.
With this, you'd be able to superglue, wire, or screw the part together so it won't fall apart on it's own, make a mold, then make the replacement parts yourself quickly and without much if any work. Hell, you could make your own phone cases pretty easy too!
http://www.smooth-on.com/Rigid-and-Flexible/c10/index.html is the site.
Goodluck, you'll need it!