Chicken with tail down and sitting a lot in the afternoon

It her belly enlarged? Fluid (ascites/water belly) or internal laying could make her breathing more labored. If she has ascites, a common problem in older hens, then there is not a lot you can do about it. You could drain her belly with an 18 gauge needle and large syringe from your feed store, and if you get yellow to dark amber fluid, that will confirm it. Draining occasionally can relieve pressure and ease breathing p, but won’t cure her. It also may cause infection or rarely, death, so not without risk. I usually don’t drain, letting nature take its course. When a hen dies, you can perform a necropsy at home, and look for ascites, salpingitis, cancer, or tumors. It is a good way to learn about what was going on. How does her crop feel?
 
Whistling exhalations can be a sign of respiratory illness, which has sometimes presented with green droppings. The answer then would be antibiotic treatment.

This link is "way beyond" what is necessary as it covers most possibilities this side of the moon. But it gives antibiotics commonly used:

http://edis.ifas.ufl.edu/ps044

A virus, bacterial infection, even worms have been known to cause these symptoms.
 
@MedusaSnake how is your hen getting along? Have you tried draining her abdomen, just to see if there is yellow fluid inside? Honestly, we might not know exactly what is going on inside the abdomen of hens until after death when a necropsy can be done, just to look at organs. I have found ascites fluid inside of hens who had internal laying, one case of cancer, crops problems, and one case of fatty liver disease. I always try to do a necropsy on hens that die, just to see what was happening. There are videos on what to look for, and you can post pictures here for opinions. Of course, most state vet labs will do thorough necropsies with diagnostics tests for a reasonable fee.
 
Update-

She seems to be doing ok. It’s molting season now and it’s getting colder in my area. Still likes to eat and drinks, walks, and pecks around. She still does the tail bobbing thing but doesn’t sit as often. I haven’t done any fluid draining yet as she walks fine and hasn’t shown any bad signs since my last update. Her comb is a bit lighter but I think that’s normal during molting months, and another hen has a lighter comb too, both are loosing feathers.
 

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