Hello and welcome to HCM.
Thanks for putting up your query over here.Bad headache,joint pain,swollen,excessive fatigue are all due to
lyme disease or bacterial
sinusitis and not because of doxycycline.In both cases,following conservatives measures may provide relief.Your doctor is right saying to wait for couple of days till antibiotics act.
If I were your treating doctor,i recommend,
-Antibiotic course with erythroycin/
augmentin for 7-10 days,analgesics like
acetaminophen,oral histaminics like cetrizine.
-Topical nasal decongestant spray.Steam inhalation with mucinex capsule.
-Local warm compress over swollen part of face.
-Intake of adequate fluids,healthy diet and plenty of rest.
-Avoid exposure to smoke and other air pollutants.
Hope this information helps.
Thanks.