Kidney Pain / Atrophic Kidney /Gallstones

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Due to pain in my lower left side, I was referred to a urologist. I've had bladder infections most of my life (I'm mid-forties now) and I recognize this pain. Usually the Macrobid prescription did its thing and I could go on.  When the pain didn't subside from what I thought was a recurring bladder infection (UTI) I had to ask my PCP for a referral. After a scope and a CAT scan, he told me I have and atrophic left kidney.operating at maybe 20%. He ruled out the chance for kidney stones as well. Three days after that the pain quickly moved to my right side and higher. A dull achy pain still but a different pain. Eventually it got so bad I drove myself to the ER where I was diagnosed with gallstones. I am now three days post op from getting my gall bladder removed, along with a hernia repair on my belly button. The pain on my left side is now unbearable. It is horrible! I called the surgeons office who referred me back to the urologists office and then around again. I just want this pain gone. How were the gallstones not seen in the CAT Scan by the urologist? Different areas of the body? I can tell you this- I know the pain is kidney related and I just need to know if it's something I should be seen for urgently? Thank you!