You will want to use either cake, pastry or all purpose flour for your cookies.
whole wheat has less gluten formation and will leave your cookies to dence.
you can add a portion say 15% whole wheat flour in place of the same portion...
You would need to mix the paste or powder color with a clear alcohol or lemon extract, that would evaporate and set your color.
Also, keep the fondant dry by boxing and wrapping the box in platic when you put it in the cooler.