In a large bowl, whisk together the graham flour, all-purpose flour, cocoa powder, cinnamon, baking powder, baking soda and salt. In a large bowl using an electric mixer, beat the butter and brown sugar until combined, about 2 minutes. Add the molasses and beat to combine. Add the flour mixture to the butter mixture and beat until well combined. Divide the dough in 2, wrap each half in plastic wrap and flatten into a disc. Chill until firm enough to roll, at least 1 hour.
Preheat the oven to 350 degrees F.
On a floured piece of parchment and using a floured rolling pin, roll one of the discs to an even 1/8-inch-thick rectangle. Trim the edges and cut the dough into about twelve 2-inch-by-4-inch rectangles, but don't separate the cookies. Score each rectangle in half crosswise, but don't cut all the way through. Using a fork, make 3 indentations in each square. Transfer the parchment with the rolled dough to a baking sheet. Freeze for 10 minutes.
Bake until the edges have darkened slightly and the dough is set and dry, 15 to 18 minutes. While the cookies are still warm, use a knife to cut them apart. Let the cookies cool completely on the sheet on a rack. Repeat with the remaining dough, rerolling the scraps once.