My 18yo son (w/cf, obviously) was dxed with lyme disease in April, with symptoms of dizziness, muscle/joint pain, and shortness of breath. Took doxy for 5 weeks, and some but not all symptoms resolved. Then he went to an infectious disease specialist at University of Penn hospital. Doctor said that the results actually showed he was exposed to Lyme sometime in his life, probably years ago, and that he never needed to be treated for it. Also his symptoms were not even consistent with Lyme -- this doctor said few regular MDs really understand lyme. He then wrote an irate letter to our CF center for the misdiagnosis. Upon further testing, the symptoms for the most part were from low cortisol (adrenal insufficiency -- see other thread). DS probably felt somewhat better from the doxy because he was culturing a number of bugs and had a sinus infection.
So -- before you start the intensive treatment -- perhaps see a specialist. However, if your son actually had the target pattern rash, or has a single joint with swelling, that is *real* Lyme, per our expert.