Could be healing crisis or severe deficiency in Vitamin B's. Did you ever get any EmergenC? It has B's in it, and it will help with the healing crisis while you kill off the baddies.
When our microbe colonies are shifting due to candida, Antibiotics , probiotics and the like, it's amazing what kinds of reactions we can have. It really brings home just how many microbes are in our bodies! Only thing to do is to drink lots of water, take probiotics so that the good guys win, and keep on keeping on.
Are you taking anything to cleanse the bowels? Oxypowder might be the best route for you. If you dissolve the disruptions you won't get acid reflux and such. Doing that plus the parasite cleanse should get you back to being comfy faster.