I think you need to take antifungals like Diflucan for 2-3 months minimum to control Candidiasis. I think they should be continued for around a month after symptoms go away. I don't think Diflucan and Sporanox are as bad for the liver as some people make out. Of course it is an individual thing. Nizoral is much more dangerous for the liver. From what I have read, most people tolerate Diflucan/Sporanox without any liver problems. That said, I would take regular liver function tests while on any of these antifungals.
The issue of resistance developing to these antifungals is a major issue though. The best idea is to get the diet and immune issues as good as you can before starting, and then if you are cured, try very hard not to get another bad candida overgrowth because the azols don't work as well second time around due to resistance.
I think the chances of success are improved if an non-absorbed intestinal antifungal like nystatin is taken at the same time as Diflucan.