The color of your menses I think has no relation with the kidney
stone which is present.
In cases of kidney stone if it is causing some bleeding because of some erosion in the urinary tract
than it will be comming through urine rather than with the menses. It may be there that you can have some change in the intensity of kidney problem during your menses because of the hormonal
changes taking place.
Now as far as the color of your menses is concern if this is something new and happening for last few months only and there are no other problem associated with it than it can be because of the changes in the pattern of your flow because of your age. I would suggest you to consult some gynaecologist regarding this change.
Thanks and take care.