I am going to answer this question as if it applies to a human. I claim no veterinary knowledge.
I am not aware of a direct connection between kidney stones and an increased alkaline phosphatase.
Alkaline phosphatase normally comes from the liver or the bones. A GGT level can be done to determine the source (i.e. elevated GGT suggests a liver source). Bone diseases can include bone growth, healing fracture, acromegaly, osteogenic sarcoma, liver or bone metastases, leukemia, myelofibrosis, and rarely myeloma.
Regarding liver causes, the most common causes include partial bile duct obstruction, primary biliary cirrhosis (PBC), primary sclerosing cholangitis, adult bile ductopenia, and certain drugs such as androgenic steroids and phenytoin. Infiltrative diseases include sarcoidosis, other granulomatous diseases, and less often unsuspected cancer metastatic to the liver.
Next step would be a liver ultrasound as well as an AMA (anti-mitochondrial antibody - suggestive of primary biliary cirrhosis). This can be discussed with your personal physician.
Followup with your personal physician is essential.
This answer is not intended as and does not substitute for medical advice - the information presented is for patient education only. Please see your personal physician for further evaluation of your individual case.
Thanks,
Kevin, M.D.