for a V6. an egg container for the lifters as you want to match the lifter back to the cam lobe. clean them one at a time. however if your rebuilding, a new cam and lifters would be recommended.
springs, retainers, rotators, and keepers do not care unless there was a single valve spring pocket that was repaired and there is a shim under it.
pushrods dont care as long as they are straight
rockers dont care as long as they are not damaged
if you have the valves out, you probably need a valve job, and that will negate the reason to put them back into their exact hole
rod caps need to be kept with the rods themselves. i normally stamp them as I take the motor apart
pistons will not get reused, and neither will the rings as you will be getting the motor bored and honed
bearings dont care because you throw them away (DO NOT REUSE OLD BEARINGS)
basically, if your reusing the lifters, those are the only items that have a mated wear surface that you need to worry about.
I am going to do the valve job myself, and by the look of the existing valves, i just need to clean them up, they are in a good condition as far as i can see prior to taking them out. The cylinders are not damaged or scratched, so i can just hone them, clean up the pistons and replace the piston rings. At least that is what i hope ill have to do. If turns out that they need to be machined, it will be a totally new price ballpark, since i want to spend as little as possible on this repair. I will have to turn the crankshaft possibly 0.001 since the engine had about 120k miles on it and therefore will have to get oversized bearings.
As for the organizing parts cylinder by cylinder, I always tried to put the old parts exactly where they came from, unless they are replaced with the new ones.
And by my early estimate, i might be ok with getting a standard marine rebuild kit for this engine: all new gaskets, new bearings, piston rings, timing chain, oil pump.
another question, what do you use to stamp the valve parts? I have a stamp set from harbor freight and i used it to stamp the pistons, but stamping rods or rockers, they are pretty small and dont want to damage them, i usually put separators into a pizza box and store pieces by the cylinder with rods in the holes in the top of the box?