Could a kidney infection that was not treated until day 3 have scarred the kidneys and cause eventual kidney stone formation? if bloodwork and cmp are normal, is that good news probably no damage?

Delay in treatment of a documented "kidney infection" by "3 days" should not result in adverse effects on the kidney(s). Many people mislabel a simple urinary tract infection for a "kidney infection". A true "kidney infection" will have more defined symptoms and lab work will be usually abnormal.

True kidney infection is called pyelonephritis. If your condition is not severe enough to be hospitalized, residual damage is less likely. However, a normal CMP does not mean no residual damage because we have 2 kidneys and they still compensate well at 49 years old. Kidney function can be in normal range by CMP even you have only one kidney as we see quite common in living kidney donors.