Yes, I have experienced the same thing. It shouldn't last long and if it does, get checked and make sure that you don't have another stone in that kidney too. Once, I had that happen and found another small stone in that kidney too. Otherwise, your other two conclusions could be correct.
How long did it take for the pain to subside? My son had Stent removal a little over 2 weeks ago and still has pain. He swears it is not as bad as the pain he was having before the procedure, but a recent sono showed small stones in kidney so I'm not sure if his pain is Stent healing or stones. Docs aren't sure either.
As the docs have obviously stated, it's hard to tell. Where are the stones in his kidney now. If the small stones have not started to move through his kidney yet, then it's probably still the stent healing. The healing time from the stent takes different lengths in different people, for various reasons.
It's your friendly urologist here.
Sometimes my patients tell me their opposite kidney hurts after having stones removed. I think this is either due to referred pain from the opposite kidney, or it could be musculoskeletal pain due to lying in an uncomfortable, flat position for a long time while under general anesthesia. Either way, if there was a problem with the opposite kidney it would have likely been caught on your preop imaging.