These Plano containers work well for storing bolts
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I also like using these Sumitomo boxes my dad gets from his work, they are very rigid and fit things like SBC head bolts and pushrods perfectly. Also you can set the top upside down when cleaning bolts, take dirty one out, clean, put in top half of box. I write on every box or part with sharpie saying what it came off of, what it is, used, etc. I have a lot of projects so it helps me keep track of them.
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For the larger parts they go where they will fit. Having another truck of the same era is nice too for reference.