I have an addiction to cashews and buy them at Costco in the larger plastic containers (they are clear, so they are great to see whatever you stick inside of them) and then use the container for the common pinball parts. The parts that are unique to the games get stored in the game in whatever little box I can find if the coin box is already full or doesn't fit everything; I sometime staple it to the bottom of the game if it would cause an issue by moving around.
I have 2 HF tool bags; one for cleaning (wax, microfiber cloths, new balls, etc) and the other one for tools. You gotta love HF!!!
pencilneck - that's a great setup you have there