Sorry to hear about your challenges. What type of food do you feed your dogs? Commercial dog foods can give dogs all kinds of challenges including allergies, skin lesions, chronic illnesses of all kinds, and even cancers. The ultimate best thing for dogs is to feed them a raw food diet including raw meaty bones, small amounts of veggies and fruits and no grains. Same goes for cats.
You may already be feeding raw, but if not and you want to know more here are some good sites to get started, one for dogs and one for cats.
You may also need to find a new vet, preferably a holistic one, who will not vaccinate blindly. If you are in the USA, you can check out this site for a holistic vet. Click on the link that says find a holistic vet.