That's a great idea.We have a wooden bead board that has 3 spots just the right size to securely hold seed bead vials. (It's #65-006 in our online store)
That gives me the idea, that if you have access to the proper wood-working tools (a router? with the proper attachments?), you could also make similar holders out of wood, for just about anything.
I usually change my mind about organizational tools about 3 times before I come up with the perfect plan.
So I really like the idea of the Styrofoam organizer/holder, as the Beta-test. Carve out a hole for the super glue, stab some holes for pliers, carve out holes for other items that commonly get knocked over, spilled or misplaced.
When the stryofoam gets too crushed (from old age or re-designs), make a new one. If you don't need any more re-designs, then take the Styrofoam piece to your nearest friendly wood-worker and ask them to make you a permanent piece (they will probably want exact measurements so they can grab the right tool ... 3/8", 1.5" etc.).
You or your SO could probably use this as a great excuse to buy new router or dremel attachments.....
--Polly