Hi.. Thanks for the query.. It looks like your son suffered from allergic reaction to Doxycycline and difficulty in swallowing can be due to congestion or swelling in throat due to allergic reaction and his tongue hurts due to inflammation of tongue due to allergic reaction.. If after stopping the antibiotic, the symptoms are resolved then it is fine but you should keep in mind that next time whenever he needs antibiotics always inform his physician about these symptoms so that he does not prescribe these antibiotics again as next times the allergy symptoms can be more severe due to already present antibodies in the blood against this particular allergen in the form of antibiotic.. If he is ok with amoxicillin then no harm in giving it for bacterial infection.. However if still his symptoms are lingering then you should consult his physician so that he can advise anti-allergics and a steroid shot.. Hope this helps.. Regards.