Do you have any pictures?
It could be mites, but I have noticed that some of my feather legged breeds get more raised scales on their feet, of there feathers are causing skin irritation.
I use a mix if stuff, but a majority is all flock raiser pellets. I have no waste. Even the cracked corn I give them they clean up of it spills out etc. I am happy with my feed usage considering number and how much they should be consuming a week. It all works out mathematically.
How are you using that much feed!? They must eat a LOT. I have roughly 60 (various breeds-but I do have some very fat white rocks and they eat and eat and eat) and two pigeons. I use around 250lbs a month.
Sorry about your flock. I lost nearly all my flock a few years ago and it is very frustrating to go through. Sounds like you are on your way to a good start. Don't be too hard on yourself.
Just wanted to post so I would be subscribed to the page. Want to make sure I can continue to learn from you guys, plus I love seeing the pictures of your guys' quality brahmas