Absolutely! I'm more than happy to help!
Molting: It sounds like they might still be recovering from molting and are working on growing the feathers in - I know that one chicken in my flock, Cupcake, still has a bare bottom! Other factors, like a possible parasite, might be keeping them from getting their feathers back in.
Stress: Sometimes when there is a change in the routine, chickens can get a little stressed out. If I may ask, do you travel quite a bit, or are your work travels less common? When you are at home, are you the one most with your chickens, or is your daughter involved when you're there and away? If they're used to seeing you, they might be surprised when they have a new care-taker...does she have a different routine than you when taking care of the chickens? (e.g. You might not cuddle the chickens that much, but she holds them quite a bit?) Did any of your chickens go broody? That might be why there are feathers in the nesting box.
Protein Deficiency: I took a look at the commercial feed that you mentioned you gave them, and it looks like it has more than enough protein. With the additional amount of protein-rich snacks, I think that it's unlikely that it's protein deficiency - do you measure how much you feed them, and do they eat at a certain time, or is it free-feed, by any chance? This probably doesn't change anything, but I thought that I'd ask.
Parasites: Although not fun, it would make sense if there were parasites, especially if they had to do with the red specks in the poop. Have you determined if the poop is coming from a specific chicken? (I know it can be hard to tell, especially in a flock with more than a few birds!) Have you noticed if the red specks are moving at all, or are they just sitting there? (In all honesty, it's not fun staring at poop, but if it moves at all, that's a good sign it's a parasite.) If you suspect that there are any parasites, make sure to keep yourself safe and clean, and consider doing a thorough cleanup of the coop!
I hope that we can resolve this soon - in all honesty, I've never heard of this before! Keep us updated, and I hope your flock will be alright!