Dear Kristy,
Given the history of a changed diet coinciding with mouth sores makes the diet a possible cause. As you change over to new food, all the bacteria in your gut undergo a conversion. This can result in irritation all along the gut, including the mouth.
Acid reflux is described more typically as a burning sensation coming up from the stomach into the lower throat. Without more information, it cannot be ruled out completely. We also cannot rule out bacterial infection of the throat or possible vitamin deficiency from the new restrictive diet.
With several of my patients papaya or pancreatic enzymes have been helpful. I am not certain whether they are giving the pancreas a rest from the new diet or helping digest the food more fully so that a person gets more of the nutrition and the bacteria in the lower gut do not.
If this situation persists, you will want to consult your local doctor.
I hope this is helpful.
Christopher Maloney, Naturopathic Doctor
Augusta, Maine www.maloneymedical.com.
Informational only, I cannot treat or diagnose via the web.
I can give you research, and research is available on my site.
I have no affiliation with Naturopathic Medicine Network, I just post because someone needs to.