Not sure if this will be helpful.
On our big trips, I have most of the spares packed neatly in to a series of lunch boxes - it's surprising just what will fit in to one box. The particular boxes I get from the supermarket and they are fairly priced. They have a silicon seal in the lid while not 100% water or dust proof, have shown themselves to be OK. The contents on that box is listed on a tag that's readable through the lid and each box is numbered. n the more remote trips, we have 16 lunch boxes + some bigger items (clutch plate, inner tubes, distributors etc), these are then distributed throughout our group. I keep a list of what parts are in which box and who has it. For my only way of packing, I draw up basic 'maps' showing just where I have each particular box in the back, so I can lay my hands on a Handbrake Clevis Pin in minutes. I've had the frustration of knowing I've had xyz part but not being able to recall just where it is.
More commonly used tools go in the front driver's side pannier box and there's a tool bag in the back with less used tools (eg, flywheel puller).
Here's 1 page from a spares list;-

How it packs in (I have the seats out here);-

and my 'map' so I can find it all !
