What kind of pain is it now?
Every time I have a dull ache in the back of my mouth, but no sign of anything odd, it usually from my grinding my teeth at night. When I am super stressed out (which it sounds like you are) I clench my teeth when I sleep and I wake up sore all over the back of my jaw. And it's been so bad once that my neck and places behind my ear were also sore.
Dentist said to have some red wine before sleeping.
Of course at the time, I was going through a breakup.
Honestly, I have no idea what's up with your mouth. But I wish you luck... and get another opinion elsewhere because your dentist seems pretty oblivious.
Now if only I could figure out why I have a sharp pain running down my right arm, I'd be all set.