My itchy wheezy puppy is acting extra itchy and wheezy

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Ok, the wheezing isn't really the problem - Astro has narrow nostrils and airways, from what I can tell, and he has wheezed constantly since I first got him.

The problem is his ear itching. He has itched off and on since I brought him home. He was taken to the vet probably 5+ times in the first month or two, to get the situation under control (he seemed to have everything going on at once - coccidia, tapeworms, fleas, diarrhea). I changed his food, added probiotics, and got his diarrhea under control; I gave him the doses of tapeworm medication and got that taken care of; he got flea baths in Dawn because he was so young, and is now on regular chemical flea/worm/heartworm preventatives.

The itching has never been really terrible, so it kind of got put on the back burner relative to his other, more pressing issues. He did get his ears swabbed and was found to have yeast, so he got EnteDerm put inside his ears for a trial period, and he now gets lots of ear cleaning with Mal-A-Ket cleaning pads.

What's aggravating to me is that his itching seems to come and go in random periods. For awhile, he'll be totally fine, and then, without a switch in food or lifestyle or anything else, he'll get very, very itchy in one ear or the other. And when there are changes, I've thought "aha, there's a trigger!" more than once, only to be left stumped again - for instance, I gave him a beef trachea and he got incredibly itchy that night/the next day, so I thought perhaps beef was the culprit, but then he snatched the second one in the pack awhile later and ate it basically in 10 minutes flat and didn't itch for days.

Cleaning his ears seems to make no difference - sometimes I'll clean them and the next day, he's itchier than he's been in a week! :confused: He has a very high pain tolerance, so I'm not sure whether he's in more discomfort than he lets on, but he never cries or scratches himself raw or anything like that - it's just a calm, annoyed digging sometimes.

I will set up an appointment with his vet after the New Year's festivities have finished. I'm just curious to know if anyone has dealt with anything similar, if it still sounds like a yeast problem or something different to you guys here, and anything else to bring up with the vet.

Here are his basic stats, for those not wanting to read the novel above.

Breed: Shar Pei mix
Previous diagnosis of the ear itching: Yeast
Foods he's been on in the past: Science Diet (what he was on at the rescue), Hill's Ideal Balance (to transition him off the Science Diet), Annamaet Salcha. I tried a couple others very briefly (TOTW Pacific Stream Puppy, Wellness Core Puppy), but he has been on Annamaet Salcha steadily for several large bags worth now.
Symptoms: Sometimes a very mild head tilt to one side, but it seems more like an itchy ear thing rather than a neurological one, because it's never tilted very far and is generally accompanied by digging in that ear.
Head shaking
Brown gunk spots - sometimes in his ears, or under his elbows, or at the juncture between his back leg and belly (though he doesn't itch these places like he does his ears)
Pawing at his ears with front legs, or digging with his back ones.
A weird, sweetish, very particular/recognizable odor sometimes.
 

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