Over The Summer Was On Antibiotics 5 Times Trying To

Over the summer was on antibiotics 5 times trying to kill an infection that I knew I had - but the Drs could not find. I sometimes thought it was urinary or bladder issues (I have interstitial cystitis) but there was slight soar throat, slight cough and once in a while a wheezing sound in my chest along with a general not feeling good. Not blood work or other tests showed up any thing until one smart dr decided to hunt for non normal bugs, and check my immunoglobulins. Amoung other things she found two pneumonia bugs, one being clamydia (?). I'm now on 100 mg doxycycline mono. 2 times daily for 90 days and in the middle of this regimen I'll be taking a 2nd antibiotic for 30 days. The die off has been a little miserable, but I am now on a trip, trying to drink lots of water, getting sufficient rest BUT yet I feel I have another kind of infection because of increased headache, lack of energy, head feeling like it has congestion or allergy symptoms, and going to bathroom 2-3 times a night ( I have for 2 weeks now) and for some reason when I take an antibiotic like Cipro or other (can't remember name) I start feeling better within 8 hours. CAN I TAKE CIPRO WITH DOXYCYCLINE and DO I HAVE TO WORRY ABOUT MY IMMUNE SYSTEM GETTING SHOT for taking all these antibiotics?! (I'm a person who lives with pAin and don't like added pain on top of pain and so I look for relief any way I can get it-- within reason). I take plenty of good probiotics, multi strain.