SOMEWHERE I've read that 12 weeks is old enough that layer won't harm them. Have no idea whether that is true. I agree, sure would like to see what a necropsy says. Staying subscribed; sure hope to get updated as this develops. It's such a mystery. A few cocci would not be surprising...
"Mixed with scratch" may be a big part of the problem. What is called scratch varies a lot; you have to read the label. Generally it has far less protein than regular feed, and should only be given in small amounts as a treat, certainly not mixed with feed.