When I read the original post my mind immediately went to kidney stones, as the pain of a passing kidney stone comes in waves. However, kidney stone pain is extremely severe to the point of vomiting. I know as I've passed a number of them, the most recent in March was 4mm.
I also had surgery on May 21 for the removal of a 1 inch small golf ball sized stone from my left kidney I did not even know was there as it gave me no pain whatsoever.
Usually with kidney stones in addition to the pain you would have other symptoms. Mine was dark brown urine that contained blood on analysis.
So, I'm inclined to believe your pain is not kidney, but probably just muscle. My best to you.