Severe skin problems.

My dog Leila started licking on 8/1/12. Her spots looked like hot spots on elbows and she consantly chewed her nails. Ears smelly and crusty.She also was licking her perianal area, and she had some straining during BM. Nails were very irritated, took her to vet, vet presecribed steriods and antibiotics. Expressed anal glands, vet said it was infected and gave her a shot ClinzGard 1.0,(8-2-12)
She got worse, smelled terrible, paws became crusty and inflammed.Perinanal area has dark colored raised area. Brought back to vet,
(8-9-12) they put her on Ketoconazole 200 mg 1 a day for 14 days-some improvement in skin
but started researching and it seems to me she has systemic yeast infection (had thyroid levels done) was a little low but vet said thats to be expected since she is fighting infection. Multile skin scrappings done, Vet never really gave us a firm diagnosis, never called to check on Leila and we already spent $1200 on x ray, tests , bloodwork etc.
and no real diagnosis. (She said possibly auto immune disease) what is that?
Well I ended the antibiotics and steroids after 14 days- took Leila off all foods and fed her just one protein source (turkey) and sprayed her with RAW apple cider vinegar, bathed her in tea tree oil and masaleb shampoo. BIG improvement, but still paws look terrible and seem painful. Negative for Lyme,ringworm,heartworm etc. Skin scrappings did show Leclercia (Escherichia) adecarboxylato
Staphylococcus, pseudinermedius, Pantoea,
her nose stared running, , limping on paws, breath terrible, called vet- she's away-they cannot see Leila , called our old vet and made an appointment for Thursday. ( we moved last year)Woke up yesterday, Leila's right leg very swollen, perianal area looks swollen as well. At a complete loss as to what is wrong with my dog, need a second opinion. (x ray showed no degenerative joint disease) she was negative for mites had been very health before the initial epsiode began with the so called "Hot spots" she did seem depressed and a little more lethargic then usual, but appetite has remained enormous. She is 40 pounds medium sized female spayed, adopted at 1 year from shelter. She had anal glands expressed in 2007, and skin infection when we adopted her (was given biotin, masaleb) cleared up (2006) other then that totally healthy. We have 2 other healthy dogs, walks several times a day, (no dog parks) Her fur is course, falling out in spots where "Fungus" or yeast is. Skin turned balckish color at those spots. She has annual vaccinations (2010 Sep) for lyme.Always kept up with her heartworm meds, flea and tick preventative (k-9) advantage 2, I feel so exhausted, and am researching everything from Thyroid issues, to flesh eating bacteria, I just don't know. Please can you offer an expert opinion?