The itching has been narrowed down to probably three things.
Allergies
Sarcoptic Mange
Liver problem causing it
I switched food four days ago so we have to give that time. Two doses of Benadryl didn't work at all so it seemed like it wasn't allergies. The vet still thinks it might be so she decided to give one injection of an anti-inflammatory to see how Ellie does. The vet was concerned about giving her anything like that because of her liver but she thought it was in Ellie's best interest to do so (because she is making her ears bleed which could be a problem), so she looked in her medical books and said one dose wouldn't hurt a thing. We went ahead with that and if last night is any indication of how it is working, it isn't working.
I will have a better idea tonight though. If the itchies don't go away we will have to do a skin scraping for mange. If mange isn't the problem we have to look at it being from her liver.