Child Has Strep Throat, Tonsillitis. Pain Is Stabbing, Blood Test Negative. Blood In Urine Test. Suggestions?

Hi there - getting a bit worried about my 13 year old son who has strep throat, tonsilitis (on antibiotics) and right flank pain. This pain can be stabbing and dull, all blood test are negative, but did show infection and microscopic blood in urine test. Doctor thought infection was showing due to tonsilitis. He is now taking up to 5 panadol a day. Went to physio as advised by doctor but physio said it is not muscular and cannot help him. He has been to 2 doctors, both gave same result, but he is usually healthy and I'm wondering if I should ask/demand a scan. Could the strep throat lead to kidney problems? Do you have and advice on where I should go from here please? I will ring the doctor tomorrow but need to be prepared on what to say and what I want! Thanks heaps for your time :O)