If the brooder got wet, something could have started growing. Cocci do like damp environments, and you haven't been doing the medicated feed, so this is certainly a possibility PARTICULARLY since you got them from two different "farmers". Small amounts of cocci could have been in their systems from their parents, and with the damp environment could have multiplied. I think treating for cocci would be wise at this point.
You didn't mention whether you were sure about the shavings or not, but it sure sounds like letting the brooder get wet may be the origin of this problem. Molds of various types can be toxic!
I'm of the "spaghetti" mindset - throw everything at it and see what sticks.
Treat for cocci, use blue food coloring in the water to attract them, add ACV to the water, vitamins, warmth, etc.
Good luck, and keep us updated, OK?
You didn't mention whether you were sure about the shavings or not, but it sure sounds like letting the brooder get wet may be the origin of this problem. Molds of various types can be toxic!

I'm of the "spaghetti" mindset - throw everything at it and see what sticks.

Good luck, and keep us updated, OK?