This is NOT a diagnosis, I just wanted to relate my experience in case it can help you!
I had a hen with these symptoms two years ago. She was passing undigested grains and had loose stools. Her urates were often discolored. I wormed her. The issue continued and she was losing a
lot of weight. We took her to the vet and the vet did a lot of testing, and my hen didn't have worms. Turns out she had
clostridium bacteria-- not botulism (there is more than one species of
clostridium) but perhaps
perfringens?
She was prescribed metronidazole (flagyl) in pill form, and it took a few weeks but my hen got better and is still with me today.
I regret I do not remember the dosage. This page has a suggested dosage, if you can get this medication:
http://www.upc-online.org/chickens/propercare.htm
It is something to consider if nothing else is working!
If you try this, when pilling a chicken, you must push the pill gently down into the esophagus. The esophagus is to the chicken's right side (your left side if you are facing the hen head-on).
I also encourage a well-rounded diet for now, if you can.... If she is having trouble with grains, you can try scrambled egg, small amounts of plain (no sugar) yogurt, cooked (soft) oats, insects such as live mealworms or crickets if you can get them... things that are easier to digest but full of nutrition. Then, ease her back onto normal chicken feed as she gets better.