Sorry to hear about your Molly getting this awful thing, but hang in there. If you have a chance, read some of the other posts on this sight & the letters pinned at the top, there's a lot of information that will help you with Molly. Although no 2 dogs seem to react the same, most do tend to get worse before they get better. It's kind of a side effect of the medication working - as the fungus in the lungs dies, it causes breathing impairment, which should improve over time. The sores are pretty common too. While my Harley was taking Itra, the vets thought doubling his dose would help & he broke out in a couple dozen sores, so they cut him back to 1.5 dose & the sores started to heal. If you check on this site, there's some posts about some type of clay used to ease the sores, but Harley's healed up on their own. They oozy eye would be more of a concern as Blasto can concentrate in the eyes & cause blindness. Some posters were pretty successful using an eye drop but I don't remember if it was an Itra or Flucon drop. That might be something to check with your vet.
Good luck with Molly & hang in there! Unfortunately, it could be a while before you see significant improvement, but sounds like your vet got meds started right away, which is a good thing & may have kept her from deteriorating as far as some of the other dogs discussed on this site before their owners could get their vets to prescribe an antifungal medicine.