I used to have a similar problem, however last year I bought a load of heavy duty large plastic stackable boxes. I now have 1 box for chainsets/pedals, another for gears/shifters, another for brakes/levers, another for saddles/posts/bars and so on... not lost a thing since! As for tools, I've got a series of rollcabs and have the rule of clean down tools (if needed) and put them back after every fetteling session haha.