How to Make It
Preheat oven to 325°F with oven racks in upper third and lower third of oven. Combine butter, brown sugar, molasses, and honey in a stand mixer fitted with the paddle attachment; beat on medium-high speed until fluffy, 3 to 4 minutes. Add whole-wheat pastry flour, all-purpose flour, cinnamon, and salt; beat on low speed until just combined, about 1 minute, stopping to scrape down sides of bowl as needed.
Roll dough out on a floured work surface to about 1/4-inch thickness. Prick all over using a fork. Cut into 24 (2 1/2-inch) squares, rerolling scraps as needed. Carefully arrange dough squares on 2 baking sheets lined with parchment paper.
Bake in preheated oven until cracker edges turn brown, 15 to 20 minutes, rotating baking sheets between top and bottom racks halfway through bake time. Let cool completely on baking sheets, about 20 minutes.
Preheat oven to broil with oven rack 6 inches from heat source. Place 12 graham crackers on a large baking sheet; top each cracker with 1 chocolate square and 1 marshmallow. Broil in preheated oven until marshmallows are browned, 1 to 2 minutes. (Alternatively, toast marshmallows over a campfire or with a kitchen torch until browned.) Drizzle evenly with caramel sauce, and top with remaining 12 graham crackers.