I am where you are. I had calcium oxalate kidney stonbes in the '80s. I was told not to take calcium supplements and to limit the amount of calcium in my diet. I did just that for 25 years until it was discovered I had osteoporosis. With that information I began researching and discovered that things have evolved since I was treated 30 years ago.
So first, what type of stones do you have? That will determine what dietary changes you need to prevent making more stones. I assume you have calcium oxalate stones given your kidney doctor said no to the calcium sopplements.
It is imperative that you drink plenty of water each day to prevent stone formation.
There is really good information about kidney stones at the following site. Pay particular attention to the part about calcium and oxalate and how it works. http://kidney.niddk.nih.gov/kudiseases/pubs/kidneystonediet/index.aspx#quantity
I have been able to stablize my ostepososis progression by adding calcium to my diet via food. According to the above web site, some researchers say taking the supplements with a meal will negate the stone building. I know how painful those dang stones are. The first one I passed was way more painful that the birth of my child. So not wanting to risk another kidney stone is understandable.
Sorry for rambling so...just thought I would let you know you aren't alone with this problem.