I'm stumped, but I'm a firm believer that there's always a reason & that that reason can be found by investigation.

If the vet you're using isn't responding, doesn't seem concerned, etc, I'd take him to another vet.

Swollen glands, itching ears, & pain aren't just "one of those things-shrug";
they affect his enjoyment of life & the cause needs to be found & eradicated.

I wish you & your kitty the best.

Hi Sylvia, the vet is okay and has checked what she considered the likely causes of his issues, but we really need to get to the bottom of this. This was actually addressed by 3 different vets and all attributed it to the stomatitis and ear mites, but obviously, that wasn't the reason as the problem persists. He is such a sweetheart and has had so many problems already, he deserves to feel 100%.

Sorry you're going through this, we have an elder cat with no teeth and I know it's no picnic.

My first guess would that maybe he's allergic to something either in his food or his environment. If he isn't already on a hypo allergenic diet, I would consider putting him on one. A lot of the foods or their ingredients are sourced out of China and you know that can mean problems.

Our puppy experienced allergy problems and it was a real challenge to find her something she liked that was both ingredient sourced and made in the USA. I eventually stumbled upon Fromm's and have experienced great success. They are a smaller scaled family owned business that's never experienced a recall. They make low grain / no grain high end ingredient foods for both dogs and cats and everything is sourced and manufactured in the USA. You may want to give their products a try. They are pricey but its worth it, our puppy is so healthy!

Here is a link that might be useful: Fromm's Family pet food

Hi Lukki, the vet ruled out allergies already because apparently they go along with persistent skin issues and diarrhea. The kitties all get Orijen or Fromm's dry, and Wellness and Weruva canned. He was on various canned foods while healing from the dental surgery and the problem was the same as now, intermittent. He can go several weeks without swollen glands, and then they swell up again. He already had this when we took him in, he was an outdoor stray, now he is an indoor kitty, so totally different environment. I am thinking to maybe ask the vet to put him on a course of antibiotics, I suppose it couldn't hurt just in case it's a really deep ear infection she can't see.

Infected salivary glands?

No, he has been checked for everything mouth-related and it's all normal since the teeth were extracted. The salivary glands are not enlarged, just one or both of the neck lymph nodes, off and on. That is why they did several blood tests over a period of time, to rule out an FIV or FelL infection too recent to show up on the pre-neuter test. But thankfully, they all came back normal. Also forgot to mention, he used to have horrible breath, but his breath is normal and not stinky at all since the tooth extraction. Also, no bad smells from the ears or anywhere else (well, except post litter box usage :o)).

Has he had blood work or tests to check for diseases involving the lymph nodes like cancer?

Yes, his blood work was normal and the vet is quite sure he does not have cancer. He has gained a lot of weight since we took him in and had his teeth extracted, so it probably isn't anything major/dangerous wrong, but still affects his quality of life as Sylvia wrote. The only lymph nodes which are enlarged are the ones in his neck, the other ones have been normal and were never enlarged during any of the vet exams. The one which seems to be enlarged most is the one on his right side. His right ear is also the one he scratches at. I really wonder if it is some sort of deep ear infection/irritation which flares up from time to time and is not visible when examining the ear.

Since I am not a cat person, is it possible the cat suffers from TMJ, which effects humans. It is a missallignment of the mandible joint.

Have you tried a course of anti-biotics, "just in case"?

not sure how your vet managed to rule out allergies.. .that would be my number one guess, as stomatitis itself is sort of related to an allergy, as is ear shaking in most cats... Just because the stomatitis is gone does not mean the allergic or autoimmune tendencies are. Allergic inflammation of the inner ear, eustachian tube and into the mouth can certainly cause discomfort though I have no idea how to determine what your cat might be allergic to (often this is the case... if not a food allergy, which it isn't' about half the time)- There are no good tests in cats to determine what they are allergic to.. and it could be 'allergic to itself' (autoimmune condition)... which is pretty hard to do much about other than treat with something like a steroid (be careful if trying steroids in a fat cat- can lead to diabetes).. had that happen with a patient of mine...got rid of the stomatitis, and for the first time in the cat's life, it was pain free... and it proceeded to gain a huge amount of weight and quickly became a diabetic... probably a more complex and difficult disease to deal with all the ramifications than is stomatitis... but at least not usually a painful one.

lzrddr, the vet ruled out food allergies based on skin problems and diarrhea occurring along with those, she never mentioned anything about non-food allergies though. I will ask her about those. I am very nervous about steroids. One of our kitties was on steroid shots for asthma and eventually came down with diabetes. We stopped the shots and she was put on aminophylline instead. This works great, and her diabetes went into remission to where she has not needed insulin shots for the past couple of years.

Sylvia, I am going to ask about antibios next appointment.

Texas, thanks for that suggestion. I will ask the vet if that could be the case.