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Good allergies or something else?

I have a one year old Australian Shepard/ Blue Nosed Pit. Months ago she received the Rattlesnake Vaccine. Both shots left her w giant puss filled bumps at the injection site. One of them actually opened and we had to drain it ourself. At the same time of her first shot we noticed a bumpy rash starting on her rear. Now months later and rounds of steroids and antibiotics later we are no closer to soothing her. She itches continuously, has bumps on her butt, tail, and sides, and ***** on her toes. Her hair seems thinned to me and falls out very easily. It's hard to tell with her merle coat thank goodness. Unfortunately I can't find a fix. We were originally on Blue as a puppy, and continued with grain free food once we saw the bumps. Now we are feeding her a raw diet with instinct. We've had a few weeks of okay skin since the last dose of antibiotics, but I can see the bumps coming back. My vet told me it was either fleas or food. I bathe her with tea tree shampoo, cover her w the best flea and tick preventative and give her the best food I can think of. My bank is busting and my puppy is still not a happy camper. I have a feeling that all of this has happened because of the rattlesnake vaccine, but at this point I'm just reaching for excuses. Please, does anyone have any suggestions?
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