to me, it sounds like she is herxing. On top of the Lyme page, you can find the thread 'New to Lyme? .... Start here!'. You can find information there for detoxing that can help her feeling better (and there's lots of other info on there).
You can do dry skin brushing on her, give her epsom salt baths (like Barngurl suggested), make her drink lots of good water with lemon (no lemon when she's having muscles spasms or twitches, it makes it worse).