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Hello. I'd like to help. I'm sorry your poor little one has been through so much!
When I first read your question I thought of a chronic Herpes infection, possibly complicated by having an immunosuppressive virus like feline leukemia or feline immunodeficiency virus. So if he hasn't been tested for immunosuppressive viruses I would certainly have that done.
And if he hasn't been swabbed for Herpes I'd think about that as well. As good as all those antibiotics are they won't change a viral infection's progression. And chronic Herpes sufferers can get destruction of their sinuses. If he's positive he may respond to L-lysine therapy at 250mg to 500mg orally twice daily. There's also new information about using Famcyclovir, an antiviral drug in herpes patients. See this link : http://veterinarymedicine.dvm360.com/vetmed/ArticleStandard/Article/detail/709697
The other possibility is a nasopharyngeal polyp. These are polyps which grow out of the eustachian tubes in young cats and can cause the symptoms you are noticing. They are usually diagnosed in cats a bit older than yours but that doesn't mean he can't have one.
And it's well worth looking by sedating him and checking his pharynx and behind his soft palate.These need surgical removal if present.
I know that you are thinking if this was viral infection my other cats should be sick and most of the time that does happen, but if they've been exposed before and are young, healthy cats they may not become symptomatic even with re-exposure.
Anyway these are just suggestions of the way I might handle this case.
Unfortunately I didn't see anything written by you before this last post. Sometimes I have the same thing happen to me too, so I understand your frustration.
Whenever I have a new kitten come in I recommend testing them for feleuk and FIV because if positive they will be affected by these diseases their entire life. If I see a sick kitten then I really think it's important. The other worry of course is that he will spread these to your other cats. Adult cats that are healthy tend to be more resistant to feleuk infections. FIV is passed by blood or saliva such as through sexual contact, a deep bite wound or from mom to babies in utero so less of a concern in normal, nonbreeding, non-fighting home situation.
Glad to hear about the L-lysine being started, I hope it helps.
I understand your veterinarian's thought about Chlamydia but as it didn't respond to any of the antibiotics, especially Zithromax, and Herpes is more common I would consider that Herpes is more likely.
Glad I could help and I'm crossing my fingers for you both that he's neg on feleuk and FIV and the L-lysine helps.
Let me know how things go. Thanks!