Sounds like you have candida overgrowth. It can take as long as 6-18 months to fully recover from candida. I have been on the diet for 7 months and am pretty much symptom free. Every week I feel better and get stronger. I have a feeling that within the next 6 months I should feel very good and can start eating some normal whole foods such as wheat, dairy, fruits, etc.
You may be able to kill the candida in your mouth, but the only real way to recover is to do a system-wide kill off and recovery. You need to kill the candida in your gut and put it back into check via the diet and probiotics.