First and foremost I would schedule a trip to the vet to have her checked for parasites via a fecal analysis. Then I would order a can of PAM (prevent-a-mite) and give her and the cage a good spray down to kill any remaining mites, as it only takes a couple to make a huge infestation before too long. After that, make sure she has a proper set-up to make her feel secure, and to keep the scale rot from getting any worse.

I would recommend using polysporin rather than neosporin, as neosporin has slight painkillers in it and isnt meant to be used on reptiles, so it can be harmful. Also, as a substrate, newspaper is excellent all around, especially if treating for scale rot as it can be changed out and cleaned alot easier than aspen etc.