When doing engine work or restoration work, organization is key to success. I recently overhauled an engine in my shop, and I was greatly aided by a careful and thoughtful organization when I took the engine apart.
I carefully catalogued the nuts, bolts, hardware and parts in zip lock bags, carefully labeled with a sharpie marker. The valve cover bolts were placed in a sandwich sized bag, labeled valve cover bolts, Left. The head bolts and miscellaneous hardware were placed in quart sized bags and labeled. These bags were then placed, in a gallon sized bag, labeled and Left.
This method continued through the engine disassembly. The oil pump bolts were bagged, and placed in the bag with the oil pump. All of the bags of parts were placed in a box with all the other parts.
When I reassembled the engine, all of the nuts, bolts and miscellaneous hardware were easily located, and the order of opening and unbagging the parts, easily gave me what I needed without wasting time searching, and minimizing the risk of placing the wrong hardware in the wrong location. When installing the left cylinder head, I grabbed the bag labeled Left, and all of the hardware was clearly labeled. When I was done, all the hardware was accounted for. There was nothing missing, and nothing left over.
Zip Lock freezer bags have an extra strong zipper, and provide a white rectangle for labeling. The next time you are in the grocery store, I would suggest buying a few boxes of sandwich, quart and gallon sized zip lock freezer bags for your shop.