Ok, this is a bit of a long backstory...

About a year ago, I took in a female squirrel, Billie. She has no use of her back legs and was raised by a fellow rehabber. The rehabber moved and left Billie in the care of her ex, who knows nothing about squirrels. It would appear that Billie somehow broke off both of her bottom teeth, which now seem to be dead, and her top teeth overgrew as a result, causing a bad abcess in the side of her mouth. This is when I took her. I trimmed the teeth, but something happened when she was eating a nut soon after, and blood was gushing out of her nose and one tooth ended up jutting out, giving her a "snaggle tooth." Now, the snaggle tooth has stopped growing as well, and we need to cut the other top tooth about once a week.
This whole system has worked out just fine until a few weeks ago, when she stopped eating. I noticed that the base of the snaggle tooth was puffy and she has pus coming out. The base was also getting a black spot that seems to be slowly growing. I took her to the vet, who put her on amoxy, but says that he has no idea what to do (which is just not helpful!). The antibiotics worked for a bit and she started eating again, but once we stopped the amoxy, the infection came back. Soooo...any suggestions?