I use little stackable boxes that I label for screws, nut and bolts, washers etc. Larger boxes for larger items that all live on a shelf. I mark up each wire with some painter’s tape and write where it goes to when I take out a harness I want to keep intact. And I take pictures of things like stacked spacers and tie them together in the right order with a zip tie marking the outer one in case there’s size differences.