Hi Jason,
There are plenty of resources online for information regarding mouth rot in chameleons. However the best resources in always an adept, experienced, knowligible exotic reptile veterinarian.
Mouth rot is the common name used to describe mouth infections in reptiles. These infections can be of bacterial, viral, fungal or parasitic origins. Other possibilities are cancer, foreign body and jaw fractures. Poor husbandry, especially incorrect cage temperatures, poor nutrition and forced feeding predisposes reptiles to mouth infections.
Trauma to the nose or mouth areas from cage rubbing or bites from live prey are frequently associated with mouth infections. Mites and ticks often carry bacteria that can cause mouth infections, especially in snakes and lizards.
If there is significant redness, discharge, or disfigurement of the mouth or nose, or if the reptile shows a decrease in activity or appetite, it is extremely important to take it to a reptile veterinarian as soon as possible. It can be very difficult to treat mouth infections after the bone and deeper tissues are affected.If it's still eating well after consultation with your regular veterinarian, some early cases of mouth rot can be treated at home with topical medications and by improving nutrition and husbandry.
Treatment of mild cases with no anorexia consists of improving the husbandry and nutrition and topical application of dilute iodine (Betadine) or chlorhexidine (Nolvasan) solution. Ask your veterinarian about the appropriate dilution.
More serious cases require topical or surgical removal of the caseous debris, nutritional support, fluid therapy.
In mild and moderate cases, if husbandry improvements are accomplished by the owner in a timely fashion, the prognosis (estimate for getting better) for recovery is good to excellent. The prognosis is guarded for cases with significant caseous debris and grave for reptiles with significant bone involvement.
Good luck with treatment. 
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CANADIAN CHAMELEONS