Regarding the two chicks: stress is also very hard on animals. Too much handling of them could make their situation worse. I know it might seem like you're "not helping", but putting them back under mom where they can cuddle and hear her talk to them might be their best shot.
Then it sounds like you have a few ideas of how you can make the rest of the hatch safer.
Heck, you could even just put a bunch of hay/straw/shavings under where the nest is so that any other chicks who fall have a very soft landing.