Agreeing with Jackie but I take activated charcoal when I am herxing as it does a good job absorbing the toxins left in the body during a die off and doesn't require a prescription. I had a test done last year that shows I don't detox well, that is why the natural charcoal helps.
It's likely a 'Herx', which is patient shorthand for 'Herxheimer reaction'. That happens when the antibiotics kill of a ton of the bacteria all at once, and then your body is left cleaning up the garbage of dead bacteria. Herxes happen worse to some people than others, and it varies in the same person over time --- it tends to lessen the longer you are on treatment, because there is less debris, due to fewer bacteria.
If these side effects are really bad, then contact your doc's office and tell them so they can decide whether you should keep taking the meds, and if so at the same dose.
That is *not* a decision I would make myself, because if antibiotics are started and stopped, it can allow some of the bacteria that were injured but not killed to develop a resistance to the antibiotic. Then the antibiotic can become worthless for you and for others.
(Antibiotic resistance is a real problem in medicine these days, because if/when the bacteria become resistant to the available meds, we are defenseless except for our immune systems, which takes us back to the days before the invention of penicillin.)
So don't decide to skip doses or to take a lower dose unless your doc specifically okays it. Sometimes Herxing can be so bad that the doc will make adjustments, but it's for the doc to decide.
You might try bathing with Epsom salts. The warmth of the bath and the magnesium (from the salts) that is absorbed through your skin is very relaxing and can alleviate the aching. Lyme bacteria use up magnesium in your body, and that can be a significant cause of the physical discomfort of Lyme (like muscle aching and cramping), apart altogether from Herxing.
Magnesium also helps with sleep.
The good (?) news is that if you are Herxing, it means the antibiotics are working!
PS about it not being an allergy to the antibiotics: you can be allergic to some antibiotics and not to others, just like different foods. If you are feeling worse than you can handle or than seems a reasonable level of misery, call your doc.
Hang in there -- !