Could it be Cocci? 5 week old chicks puffed up seem sleepy Need Help!

My one sickly acting chick seems to be more active now, and I haven't seen anymore of the really bloody droppings since Saturday, though I've seen a few that had a bit of blood. All the chicks are eating and drinking. The Sulmet is now down to half dose, and I have 2 days left on the dosing schedule, so I'm hoping that they're out of the woods. I've been keeping some powdered milk in their feed, as well as a small bowl of the yogurt/feed mixture.

I dumped out all the shavings in their sleeping cage yesterday and replaced them with fresh. Should I try to replace all the shavings in the dirt bottom of their little chick run, too? I've just been adding fresh in with the older shavings on occasion. The chicks dig around in them all day, so they get mixed in with the dirt, and I'm not sure how well I'd be able to clean all of them out. The shavings in the run don't seem to get that damp (except when I have to walk in there after going through wet grass. I have a tarp attached to the side facing the yard (and a big piece of heavy plastic tarp on the back as well) to keep any blowing rain to a minimum. The top is covered in tin, as well as under some trees (in the woods). The other two sides are only covered with wire, but are protected by the surrounding trees.

All of the chicks seem really active now, moreso than before, and when they see me bringing the little bowl of yogurt goodness, most of them come running to the front of the pen. I had no idea chickens loved yogurt (and it's plain at that) so much!
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