I recall that the highways maintenance teams who work on gantries over live traffic have thier tools on strings attached to their belts (so they can't drop them on a passing vehicle).
Apply this here - take tool from box (with cut-outs and shadows), and clip it on the belt string. Or to be fail-safe, have each tool pre-attached to the box with a long string each, but things could start to get a bit tangled up...
For the modern techie solution, attach an RFID chip to each tool, and then a scan of the box and/or aircraft will locate/stock-take all tools.