I once spent seven months and about $7,000 rebuilding a Honda Superhawk. About two of those months were spent looking for some d@mned little dowel pin or f-wording washer. But then motorcycles have a LOT more fasteners and little pieces than bicycles.
It made me a huge fan of transparent plastic drawers & bins, which can be found cheaply at fabric & sewing stores. The clear drawers make finding parts & tools a snap.
And for the little-bitty things, I like the little benchtop-jobbies. Some of them are even modular-customizable, so you can create the perfect sized compartment for your shims, cleat washers & screws, and headset spacers.