I would use .040 or .060 PETG (the stuff 2 liter bottles are made from).
I'd use it on thin tools, and add something to each tool to make a finger hole in the tray.
I may need to try this with my measuring & layout tools - they are thin, and I don't want them to have much movement in the drawer.
That vacuum former would work, but your wife may get pissed about the smell in the kitchen.