You can't treat (prevent) every different kind of kidney stone with specific measures at the same time! It would drive you crazy. If you at least had an x-ray the doctor should be able to tell you if the stone showed up or not. Some stones are visible on x-ray and others are not. That would narrow it down, at least.
The vitamin D issue only applies to oxalate stones, and it's not that you can't take vitamin D, just that you should take the calcium supplement (without vitamin D) at a different time (as I understand it). A low oxalate diet can help, too, but it's complicated.
Drinking plenty of water is important for all J-pouchers, but it's even more important for those prone to kidney stones. Stones form when *something* is concentrated in the urine, leading to crystal formation. Plenty of water ensures that nothing is in high concentration in the urine.