Could you substitute molasses for the maple syrup? And use gluten free flour?

You probably could substitute molasses, but you'd have a much, much different cookie, that would taste a lot like molasses. The molasses would also very likely overwhelm the flavor of the pecans, so I wouldn't make that substitution.

I would however substitute King Arthur Baking's "Measure for Measure" gluten free flour blend substitute. I've had great success with it in every cookie, brownie, quick bread and bar recipe I've ever tried using that product instead of all purpose flour. ;o)