to stitch them in, you'd have to take everything apart, but you could applique cornerstones in on top of what you've already done...do something fun if you want - set them on point, or just put them in wonky to add some fun to the quilt. You could also applique completely different shapes.
Beautiful job, by the way. and remember that you don't have to always do it just as the book says. As you quilt more you'll see things that you like better (or less) than what the book calls for and it's OK to make those changes. for example, if you like the look you have here - leave the setting stones out.