Preheat oven to 350 degrees. Butter a 9-inch square cake pan; line with parchment paper, allowing a 2-inch overhang. Make the cakes: Whisk flour, wheat germ, baking powder, cinnamon, and salt in a medium bowl. Put butter, brown sugar, and honey into mixer bowl; mix on medium-high speed until pale and fluffy. Reduce speed to medium; mix in eggs and vanilla. Add flour mixture; mix until just combined.
Spread batter into prepared pan; smooth top. Bake until golden brown and a cake tester inserted in the center comes out with only a few moist crumbs attached, 25 to 30 minutes. Let cool in the pan 15 minutes. Lift out; let cool completely on the wire rack. Can be stored, wrapped in plastic, up to 1 day.
Cut out 8 rounds with 2 1/4-inch cutters and 8 rounds with 7/8-inch cutters. Transfer to a baking sheet lined with parchment.
Make the glaze: Put chocolate in a small bowl. Heat cream and corn syrup in a small pan over medium-high heat until just simmering. Pour over chocolate; stir until chocolate has melted. Let cool, stirring occasionally, 20 to 25 minutes.
Spoon a dollop of glaze over each cake and large marshmallow, spreading so it runs down the sides. Stack: large cake, large marshmallow, small cake, mini marshmallow.