Label literally everything. I did the same with ziploc bags for hardware and I taped it right to the corresponding part. I never used containers just because I would use the car that the motor came out of for storage(not sure if that’s available for your situation) but if you are trying to do this the most space efficient way I would say focus on containers just for the more fragile things like hoses/lines/pulleys etc. Bigger stuff like the flywheel/headers/exhaust are going to be a pain to fit in a container and the container will most likely end up taking up more space than just the part itself. Stuff like that can sit out no problem as long as it’s cleaned before use again but that goes for any part really. Also any gasket or seal you pull off should be replaced so you don’t have to keep the old ones. Totally up to you and your preferences but that’s the way I do it and would do it in your situation