A Herximer reaction is common when on a treatment program with antibiotics for lymes. Some doctors use the herximer reaction over blood tests to accurately diagnose lymes. I have found taking activated charcoal a few hours "After" the meds to help with the die off if it gets too bad. You don't want to take it too close to meds or vitamins or it will soak it up like a sponge. I also take chlorella as well....it helps clean the bloodstream.
Heightended Lyme symptoms while under treatment from antibiotics ( doxycycline included) is a very common manifestation. Starts with an H as I recall...
Anyway it is mentioned in most Lyme books and elsewhere on this Forum.
I've felt immediately better when off doxy and then over time it comes back.
Maybe better to stick the doctor's program -- so that the cycle of the Lyme is addressed.
I had a reaction to some other Lyme antibiotics I was on, after I had been taking them for several months. The dr pulled me off of them and put me on something else, but I don't know what caused the 'reaction.'
I took a little treatment holiday before beginning the new meds, and felt better during that holiday than I have in years -- but began to go downhill again in a while and am now back on the new drugs. Perhaps what is going on is that you feel lousy from the disease itself, you feel lousy from the die-off of the disease while under treatment, you feel lousy from the side effects of strong meds, and it's hard to tell which thing it is. Maybe all of the above. Let us know what the dr says.
Good luck!