Normally I stay clear of things I know nothing about, but I thought I would throw this out there since my mother had very similar symptoms much of last year. She started out being diagnosed with oral thrush and bad heartburn as well as low b12, but after alot of these things were treated successfully, she was left with something called Burning Mouth Syndrome. Compounded with the heartburn, it sounded alot like what your wife is experiencing.
It's a long shot, but since it's one of those things that doctors don't seem to know about, we have to educate each other. It's a very real medical condition and it drove my mother cuckoo-bonkers until she found out about it on her own.
Good luck and keep us up to date on her progress.