You say the fluoride is painful? What is the brand and type? Hoping I don't get in trouble with the moderator for promoting a product, but in Canada they sold me a neutral pH 0.5% sodium fluoride gel called PCxx Anticaries Topical Fluoride Gel, NPN#02149923,
www.rosshealthcare.org, and it truly was pH neutral and didn't sting at all. It's made in Canada but also marketed in the USA. I think this might really help.
I can't get this product now that I live in England, and have had to drop back to Colgate Fluorigard Gel and to this day (nearly 1.5 years out) it stings somewhat.
As for the sores, well, as many will say on here, keep the faith, they will go away, eventually. For quite a while post treatment anything acidic would trigger "water blisters" in my mouth when my secondary salivary glands would try to squirt through the damaged mucosal skin layer inside my mouth. I couldn't eat even a cherry tomato for several months. But this doesn't happen at all now, and I had forgotten all about it.
Good luck!
-Seth