10-year-old With Kidney Stones...scared!

Hello, I am desperately searching for answers. Four weeks ago, my 10-year-old son had severe pain in his lower right hand side, by his pelvis. We went to the pediatrician. He suspected appendicitis, so we went for a CT scan. Appendix was fine- but the CT revealed a kidney stone that was 2 mm in size. We were told to strain his urine to catch it. We waited and strained and he was out of school. Finally, after 7 days, I sent him back to school thinking it must had passed and we missed it (he was sore, but no terrible pain) , well at school he passed it- he saw it come out. It was dark brown. So we didn't catch it. He was pain free for 24 hours when the exact same pain developed on the other side. We went to the pediatric urologist 2 weeks after detecting the first stone. They did a simple blood test - he said everything came out fine. They did an ultrasound and KUB x-ray...they said all that looked good. There was no sign of the stone in the other side, but my son was still in pain and he said it was the same pain as before, so I just know he has another stone. The urologist said he didn't want to do another CT scan because that would expose him to more radiation. He said to just keep straining the urine...so now, 3 weeks after the first pain from the second kidney stone, my son is in terrible pain. He was on his hands and knees crying last night. He said it hurts so incredibly bad when he urinates. The urologist was no help in determining what may be causing this or how to stop it. Should we go to a nephrologist? I feel so helpless without any answers from the doctor. Thanks!