Are you giving any ibuprofin? That may help calm things down a bit. Also may I recommend an excellent probiotic?We use Florastor Kids. My dd10 has PANDAS,Lyme, Bart. and Mycoplasma. She has taken a cocktail of antibiotics daily and the Florastor has protected her gut!
As far as herxing reaction, I would make sure you have touched based with your Dr. Watch the foods your child is comsuming, food dyes and artificial ingredients for us have often led to behavioral changes and nightmares - specifically red dye for us.