Thank you - that paints a much more clear picture of what was happening.
First, I think the first batch of deaths, and the second batch of blisters are possible separate.
I think that the breast lumps are actually "breast blisters" which are like the ones commonly found in broiler houses. The breast bone (keel) has a small fluid lined sack that has a membrane protecting it. If irritated, often by environmental factors, it can become inflammed and infected. The causative agents (bugs) are often Mycoplasma synoviae (not to be confused with M. gallisepticum), Pasteurella, or staphylococci. Staph is commonly found in the ground anyway.
Wet conditions, keel bone irritation from sharpness, pretty much a range of conditions in the environment can cause this. It's common in broiler houses where birds are housed in close contact.
The blisters can apparently be fluid filled - clear or blood tinged. Does this sound like it? Here's a picture:
http://www.poultrynews.com/New/Diseases/Merks/204702.htm
From what I can see, most often if there's treatment at all, it's by puncturing the blister with a sterile instrument, and treating with some sort of potassium solution or antiseptics along with systemic antibiotics. Because we don't know the exact causative bacteria, I wouldn't want to treat systemically. I'd like to know more about the puncturing treatment before I'd try to describe it. But that seems to be the only treatment ever given.
I suspect that the chicks died of something more common to chicks. You say their droppings were dark brown with white - but were they runny dark brown consistently, or solid? There are a number of factors including brooder pneumonia, temperature issues, illnesses, even just a weak line of birds. There could have been a bacterial infection since you said that 2 days of litter was very smelly, though it's usually smelly so too ahrd to tell there. It could have been dietary insufficiency, or anything.
I'm wondering about coccidiosis because of the water spilling, or aspergillosis (brooder pneumonia). But usually breathing issues are associated with the latter, and there's just not enough of a visual for me on the former though coccidiosis doesn't necessarily have to include bloody droppings. Sometimes it's just loose droppings and cecal involvement. There are different forms of it. So it's hard to tell.
What it seems like to me is that there were a number of deaths in quick succession - and then a break, but keel issues and the rooster that has a reduced immune system and keel blisters? yes?