After building and modding numerous cars, I found that my well-organized bins were getting less and less organized, and when I found myself looking for four matching bolts, I'd seem to find 3 nice shiny ones and one pitted, rusted one.
I'm kind of "between" major projects right now. So, I recently hit up a buddy who dismantles S130's and Z31's and bought a 5-gal bucket of hardware from him. I also emptied out my bins, which filled another bucket.
After sorting through and taking out all the junk fasteners and non-metal bits, I separated the stuff into 3-lb batches. Each batch went into a "boiler" which I made from a stainless steel cooking pot, a stainless strainer, and a single electric burner. I added a scoop of Cascade, a slosh of Purple Power, and enough water to submerge the hardware. After bringing it to a boil for 30 minutes, the hardware can be dumped out - all the oil, grease, and funk will be gone, and the parts will "flash-dry" from the heat.
Then, everything went into a container to head to the plater. For about $125, I can get a 5-gal bucket of fasteners plated with zinc. I prefer the yellow zinc. Typically, anything that can be barrel-plated can be in the same batch. Larger parts have to be rack-plated, which costs more. They'll acid-wash everything before plating, which removes even more of the "gunk" and creates a smooth surface for the plating.
Here's what everything looks like when it's done:

If you look closely, there are some hose clamps in there - those turned out really cool!
I'll be running another load here soon, and then I get the awesome task of sorting it all. I bought one of these off Amazon.com:

This one is handy, because you can take it with you to check fitment, even if you're under a car or clear across the garage.
I'm thinking this will save me a ton of time on the next project - Thought it might help you guys as well.
Post up your hardware management ideas here!
