I use and highly recommend a product called "Yeast Ease". It is one of Dr. David A. Jernigan's products and sold online. If you are interested in checking it out... google, "The Hansa Center" and check out their eStore. Dr. Jernigan regularly treats lyme patients and has lyme disease himself.
I'd be thrilled if others have more to say on this topic. I've read elsewhere that people go to extreme measures to combat systemic yeast infections, and that the symptoms can be as bad as those from Lyme. But from what I have read, I can't decipher how serious, likely, detectable, or treatable candida overgrowth can be.
My LLMD has not said much about it. I take a probiotic, but have not been advised to make any changes to my diet. I've read that if yeast is a problem in you that you should avoid sugar and white carbs. That's about all I know.
I'm still learning about ammonia in our brains, low thyroid and other problems that many CFS and lyme patients have. I'm too brain fogged to figure out the ammonia stuff, but Jernigan discusses it in his book and on his website as well. (Hansa Center)