Good Morning and thank you for writing in to Just Answer!
It sounds like overall your 15 year old dog has been doing very well for her age! I am sure this ongoing coughing and sneezing is getting frustrating for you and her, however.
Of course I can't diagnose her online, but I can offer you my thoughts based on what you have described.
Based on the symptoms and the fact this has gone on chronically (3 months), I would have a couple of thoughts: Respiratory infection (such as upper respiratory, sinusitis, or infectious bronchitis, or even pneumonia) and/or chronic bronchitis.
I don't have access to her full medical records and all that has been discussed or done, but I certainly would be concerned about the possibility of bacterial infection, simply because she has had eye discharge and wet sneezing and coughing for 3 months and this has not resolved fully. Sometimes the x-rays on dogs with these symptoms may not show much. In those cases, based on the symptoms and the length of time this has gone on, a course of antibiotics would not be a bad idea to assess response. Of course, diagnostic testing can also be done first, such as transtracheal wash, which one of your vets suggested. This sample can be cultured to see if infection is occurring and what type of infection.
One type of infection that really comes to my mind is Mycoplasma. This is an unique type of bacteria that can cause a lot of respiratory signs, such as coughing, sneezing, and red gunky eyes (conjunctivitis). I would be suspicious of this especially in your dog. In my experience the x-rays in these dogs may look pretty normal. In those cases if we suspect mycoplasma infection we may just treat with appropriate antibiotics. here is some information on that type of infection:
A very common cause of chronic coughing in elderly dogs is Chronic Bronchitis. I also wonder if this might be going on with your dog. In fact, sometimes a dog can have underlying chronic bronchitis (causing coughing) with a secondary upper respiratory infection, for example. Here is some information on chronic bronchitis in dogs:
Chronic bronchitis causes a cough that is mostly worse at night, like you have described, and would be a very common cause of coughing in a 15 year old dog.
In any case, your dog's symptoms are not normal and certainly warrant further investigation and treatment. I hope you can find a vet who will be able to help you with this! Thank you again and I hope this information has been helpful. Please let me know if you have further questions!