Ear itching/head scratching issue not solved

So at my cats annual exam about six months ago I told the vet that she was scratching at her ears and shaking her head often. She is an indoor cat who is not exposed to other animals. 

The vet checked her ears and saw no sign of ears mites. 

A few months later we dealt with a rodent mite issue in my apt, which I worried might transfer on the cats fur. The vet had me buy a 7 month supply of Revolution to give her. 

After her second treatment she dug two large sores and lost fur in large patches on her back. 

We have since moved so the rodent mites are no longer an issue since they have a 2 week shelf life without a host mouse in the walls. 

My vet has told me that she must have had a bad reaction to the revolution, stop giving it to her and to call the company to complain. 

She's not really helping with the fact that Coco was having this issue long before the mites came to be and still is. 

What are reasons that a cat would be shaking her head like this and scratching if she is clear of fleas and ear mites? 

I'm also confused at why I was given revolution if it doesn't kill mites at all which was my concern during the apartment drama. 

Could have a yeast infection in her ears.  Is there any brownish discharge or buildup?  It could also be airborne allergies.

Nope-no smell or noticeable discharge. Who knows maybe she's just itchy. 

Have you fed the same protein for a long period of time?  My kitty had this issue and it turned out he had developed a chicken allergy.

Cindy had a yeast infection in her ears and was exhibiting that behavior (scratching and shaking her head).  There was no discharge or anything like that. The vet had to take a culture to determine what it was.  A round of ear drops cleared it up nicely.