What Causes Stomach Pain In A Child While Having Elevated PH/protein In Urine?

My 6 yr old son was born with Hydronephrosis. he is now anemic. He was recently saying his stomach hurt, most often before school in the morning. However, just to be safe I took him to the doctor. they did his normal blood work due to the anemia as well as a urine test. His urine came back with 1+ protein in his urine and the ph levels were slightly elivated and the doctor said this is typically the result of children needing more water. However, he drinks a lot of water. Today he urinated, and five minutes later had to go again, then 7 minutes after that went again. After the three times he waited 20 minutes and went again. He says his right side has been hurting now since yesterday when he feels like he needs to go urinate. I plan to ask his doctor to refer him to get another ultrasound on his kidneys tomorrow because I just do not have a good feeling about it. what is your advice?