Why is my left side painful or sore after a right side perc stone removal?

Shouldn't be. Having a procedure on the left kidney should not cause right kidney pain. The pain on the other side may also be from the positioning of your body on the or table during the procedure.
Possible early stone. Also, you may have been lying uncomfortably during the procedure for the other side stone and now you are having musculoskeletal pains that will last for a few weeks and resolve. If the pains are not getting better, you need to address it with your doctor. You may have a very small stone in that side, that is moving some, and causing the pain.