Thanks Florcraft. We took up the carpet and found that the stones are on a base that is about the height of the flooring that we are putting down. (Don't know why we didn't think of this first.) We should be able to get the flooring under the stones and hope to make it look decent. It will still probably need the grout as you suggested though. I wasn't sure what to fill it in with.
I just wanted to say that I am so glad I found this site. We are remodeling after a flood and there are so many good ideas that we sure can use.