The inner tube is a good idea. I've used it before for lots of things, never bothered to try and glue it together though.
I pack my bits and pies in small 4 1/2 " x 8" x 2 1/2" plastic tupperware style boxes, and make sure everything is tightly packed, and delicate stuff separated by bits of rubber sheet much like inner tubing.
Trying to make each item perfectly packed is too much like work. I've never had any problem with the packing method above.
Electronics etc do well this way, I make a point of having a "delicate" box and a non-delicate box, and pack them appropriately in the panniers.
I don't put my spares in with the tools, preferring to have access to the tools separately and the tools packed forward because they're really heavy!
I don't pack sockets as you've described, just toss them into a heavy cordura nylon pouch loose. Easy to get at. Same cordura pouch went around the world, minor abrasion / possible holes developing, but the same pouch was already ten years old before we left... I also use a cordura tool roll for everything else, as well as the genuine BMW tool roll. Two separate tool rolls makes it easy - the common quick stuff for side of the road repairs, and the other if we're gonna get serious.
the tool rolls work great, highly recommended, no rattling, easy to find tools, someplace to put small parts, and both rolls are still in perfect condition.
Frequently needed and emergency type stuff / spares like tape, wire and fuses and patch kit are kept very accessible in the BMW's underseat tray.
Waterproofing should be adequate with the tupperware boxes so you don't have to worry about the electronics - besides, so long as they're dry before you use them it's not the end of them if they get wet along the way. You do want to keep them dry because of the risk of corrosion, but it's a minor worry, don't go to a lot of trouble past plastic boxes.
have fun sorting it out!
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