I'd finish out the course of the drugs and see how he does. I can't believe the vet wouldn't run a fecal on him. He could, probably does, already have parasites from being fed live or fresh killed somewhere along the line.
I don't know about the mouth rot. That would be a good question for the vet- what causes it.
Be VERY careful to keep him in isolation from your other snakes. Make sure you care for him last.
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