Preheat 350°F, put rack in the middle position. Bake a sheet of crackers for 8min, rotate pan, bake another 8min. Cool crackers for 5min on cookie sheet. Gently separate warm sheet along perforations into separate crackers, and cool completely on wire rack.
In a large bowl, whisk together flour, wheat flour, wheat germ, brown sugar, baking soda, salt, 1 tsp cinnamon, and nutmeg. Cut up butter add to bowl. Cut the butter into flour mixture using pastry blender.
In a small bowl, whisk together honey, milk and vanilla extract.
In a small bowl, whisk together sugar and 1 tsp cinnamon.
Add honey mixture to flour mixture, and combine with hands. It will be soft and sticky. Gather dough into ball, and divide into four pieces.
Between two sheets of floured wax paper, roll out a piece of dough, until it is roughly rectangular and 1/8in thick. Remove one sheet of wax paper, and use a pie crust wheel to cut 2” squares in dough. Peel up the dough of any irregular pieces, and return to bowl for reuse. Using a toothpick or skewer, prick dough to make five holes in each cracker in the normal graham cracker pattern. Sprinkle lightly with granulated sugar mixture. Stack layers of dough/wax paper onto a cookie sheet and put in freezer for 15min.
Once dough is cooled, process one sheet of cookies at a time. Place one sheet of dough/wax paper on a cookie sheet. Bake as instructed above.