Have you tried using an organic toothpaste? I switched a number of years ago. I didn't notice any difference, however I know they are considerably healthier as they contain no fluoride, SLS, Sugar or preservatives . Some people have allergies to fluoride and SLS. I am sure you have already seen this info around though.
I was using straws, but now I shot everything so that nothing touches my lips. I also use a bottle and pour my coffee in there to swig small amounts of liquid into my mouth.
I have tried an ointment called Keracomb. Which is an anti bacterial, anti yeast, and anti candida albicans. It did not help, only made the skin come off more easily. It may help for you however. It has a vaseline like consistency.
Thats cool you are exercising 3 days a week and taking a multi. I have been in a pretty bad spot so have been quite lazy in terms of diet and exercise. For the past 6 years I had been what you would call obsessed with healthy eating and living; spending $1000s on the best supplements you can buy, exercising and following a paleo diet. None of it has helped though, so I have given up a bit lately.
What I have learnt is that the only way for me is to leave them alone and let the body slowly heal. Its quite obvious that if nothing has worked than this is the only way. I was looking for a quick fix, hoping to wake up and be cured. You can't cheat this though.