Combine softened butter with brown sugar, honey and vanilla extract in a large bowl or the bowl of a stand mixer. Mix by hand using the "creaming method" with a wide rubber spatula to smear the butter and sugar together and mix vigorously until smooth, creamy and slightly fluffed. You can also use a handheld mixer. If you use a stand mixer, secure the paddle attachment and mix on medium-low speed for 2 minutes. It should look more like a paste or damp sand rather than a very pale aerated mixture. Add the egg and mix until well incorporated.
Combine both flours, baking soda, cinnamon and salt in a medium bowl and whisk to blend evenly. Add the flour mixture to the creamed butter mixture and mix until just incorporated.
Add chocolate chunks and marshmallows and fold them through the dough.
Use a 1.35-oz cookie scoop to portion dough and roll into smooth balls. Place crushed graham crackers in a small bowl and press cookie dough balls into the crumbs but don’t roll around all the way. Place dough balls onto the prepared baking sheets spacing them at least 3 inches apart with the graham cracker side up.
Bake for 9-11 minutes until evenly golden and still soft in the middle. Let cookies cool and set completely on the baking sheets since the marshmallow that oozes out is very sticky while warm. Sprinkleflaky sea salt on top while still warm if desired.