Hi there. I am currently going through the same thing. Apparently I have had thrush for 4 months. It is getting better but I am still sore. I have used Gentian Violet; however, make sure to put vaseline on your baby's face so that his face doesn't stain. It fades pretty quickly. I went to a lactation consultant at Maternal Expressions in Folsom and she said to do the gentian violet for 3-4 days and then re-evaluate. I used it at night before bed. In addition she told me to use what they call All Purpose Nipple Ointment (Polysporin, Miconozole, and Cortizone creams mixed together and lightly coated on the nipple 3 times a day except when using Gentian Violet).
***I found Gentian Violet at Bel Air/Raley's for $3.50, Long and Walgreens could order it but it was around $8.00 and since I had to get it on a Friday, I would have had to wait until Monday to get it ***
I also found this website that I am following, as I am trying to cut some sugars out of my diet as well due to the yeast feeding on it. http://www.oz.net/~chotii/fighting_thrush.html
If you have any more questions let me know. So far it is working, slowly, but it is working.
Good Luck
***So I finally got tired of being in pain and having a purple mouthed baby. My doctor put me on Diflucan and I have been on it for 1 week and already I feel 100% better, I am starting the 2nd week of meds because I am prone to yeast infections as it is and I want to make sure that it is all gone before I stop taking the meds. The DR. stated that in worse case scenarios the meds may have to be taken for 4 weeks.****