Had to think back to when I was doing them 'the hard way' and things I found really useful were beer flats.
No, not the beer, the low tray boxes, that can goods come in.
I could lay the stuff out in the boxes and stack or move the boxes, keeping things together.
Worst things I have used were deep boxes. The little stuff gets lost, things get banged together.
A number marker of some sort, even if it's a sharp awl is essential.
I always stamped pistons on the front.
I have opened engines, freshly rebuilt, that had the pistons in backwards three times.
Baggies seem useful, but I haven't had good luck with them. Oily fingers and parts, smear up the bag, the bags have nothing to tell them apart, etc.
Mark the piston before pulling, pull the piston and put the rod cap back on right then, finger tight. May feel like it takes longer, but it shortens the time of the whole job. Not sitting going um, didn't this belong to that one?
If it's going to be a long time before you put it back together mark every hose, line, etc.
An old pro will just laugh and know where everything goes. You won't remember a week from now.