In addition to Jey100's always excellent resources, you might have yourself tested for the MTFHR genetic mutation. I know two people who have CFIDS/Fibro, one of them my husband, and they both had some variation of it!

http://mthfr.net/

In addition to a low-carb diet, there are some supplements that can help a lot. And gluten-free gut healing is absolutely something to look into.

Artificial sweeteners, for instance, are considered "allowed" on an Atkins plan... unless they stall people or otherwise cause problems. And you say Atkins-ish. Let me just guess you aren't a strict meat & vegetables person?

That alone might be a problem in adapting to your new, more healthful, regimen.