Make the cookies: Whisk together flours, wheat germ, salt, baking soda, and cinnamon.
Beat together butter, sugar, and honey with a mixer on medium speed until pale and fluffy, 2 to 3 minutes, scraping down sides of bowl as needed. Reduce speed to low. Add flour mixture; beat until combined.
Turn out dough onto a floured surface, and divide in half. Roll out each dough half to 1/8-inch thickness, and refrigerate until firm, about 10 minutes. Preheat oven to 350 degrees. Cut out squares with a 3-inch fluted square cutter. Cut a star out of the center of half the cookies using a 1 1/2-inch star cutter. Reroll scraps once, and repeat.
Place squares 1 inch apart on parchment-lined baking sheets, keeping cookies with cutouts together. Refrigerate until very firm, about 15 minutes.
Bake cookies until dark brown, 14 to 16 minutes, rotating halfway through (star cookies take about 1 minute less). Let cool on sheets 10 minutes. Cookies can be stored in an airtight container up to 2 days.
Assemble the s'mores: Preheat grill on high (if using a charcoal grill, coals are ready when you can hold your hand 5 inches above grill for just 2 seconds) or build a campfire. Divide chocolate among cookies without cutouts. Skewer marshmallows; toast over grill or fire, rotating, until gooey in center and nicely charred, about 2 minutes. Remove marshmallows from skewers; place 2 on each chocolate-topped cookie. Sandwich each with a cutout star cookie; press gently. Let sit 2 minutes to melt chocolate.