Rebecca, if the glass is colored during glass processing and not painted or coated after production, CLR is only safe to use on the glass. If you avoid any contact with the lead or frame of the stained glass, CLR is safe to use as a dilute solution of equal parts CLR and warm water. Apply the solution to the glass only with a damp cloth or sponge. After 2 minutes, remove the solution from the glass with a damp cloth or sponge and clear cold water.
To ensure that the CLR solution does not come into contact with the other materials in the stained glass piece, do not spray directly onto the glass.