Talk to Nephrologist on Kidney Pain Yet No Stone

1- I had 1.7mm stone (Calcium Oxilate) in right kidney. Got it removed by 2 lithotripsy sessions with stent placed. Afterwards stent removed.I started fasting and fasted for 9 days of Ramadan. 2- But 2 remaining calculi of 4.5mm and 3mm remained, that got extracted with pain in ER after 9th fast. Afterwards Ultrasound shows clear and healthy kidney. 3- After resting for 2 days, that I started fasting. After 2 days fasting, I started having blunt pain in right kidney. Ultrasound all clear. Pain remained for 2 days and went away. Took medicines as Urologist prescribed and all went well. Started fasting after 3 days rest. Also started black coffee 1 large mug a day. 4- For a separate muscular issue, Orthopedic prescribed Vita-D3. Took that and pain in right kidney started 10 mins after that. Drank lots of water to get hydrated yet the pain resides. US all clear. I cannot find the reason of pain. Can Vita-D3 or black Coffee or Dehydration be the reason? Please can someone help me find