Sorry you've been ill, but it's good that you are being treated by a competent doctor.
A temporary flaring up of symptoms, known as a Jarisch-Herxheimer reaction or herx for short, is normal. This occurs due to toxins released by the organism as it dies off. Borrelia burgdorferi (Bb), the Lyme organsism, has a four week reproducive cycle and much of the dying off occurs while the organism reproduces. For this reason the herx is typically most severe at four week intervals but can occur at other times.
Were you tested for or does your doctor suspect co-infections? It is important to treat for any co-infections, the success of Lyme treatment depends on this. For many of us, getting co-infections under control has been crucial to treating the Lyme.
It is important to take a quality probiotic while in treatment to maintain healthy levels of digestive bacteria to minimize upset. The best ones I've tried so far have been Jarrowdophilis EPS and another one called Primal Defense. Neither of them requires refrigeration so you can carry them with you.
Many people have experienced at least a little relief with detox baths during herxes. Add 1-2 lbs. epsom salts and about 8 oz. hydrogen peroxide to comfortably warm/hot bath water. Try to stay in for 20-30 min., if it is too hot or too cold you can adjust the water accordingly. Drink as much water as humanly possible, at least a gallon a day, to flush out the toxins as well as to help your body cope with being on high doses of medications.
Be sure and avoid sun exposure while on doxycycline, it is possible to get a nasty burn even through a window.
Good luck, the beginning of correct treatment is the first step toward recovering from this.