In a small bowl, mix together flours, wheat germ, baking soda, cinnamon and salt.
In a large bowl, mix together butter, 2 tablespoons peanut butter, honey, vanilla extract. Add dry ingredients and mix until a dough ball is form. Add a tablespoon or two of water if dough is too dry and crumbly.
On a piece of parchment, roll dough out into 1/4-inch thickness into a 12×10-inch rectangle. Use a pizza cutter or knife to cut into 1×1-inch square crackers. Pierce with fork tines for decoration.
Put parchment paper on a cookie sheet and bake in oven for 10 minutes.
Re-cut the crackers and cool completely on a wire rack.
To make sandwich crackers, spread 1/4 teaspoon of peanut butter on one cracker and top with another cracker. Repeat until all crackers are used.
Store in a plastic bag or container in a cool, dry place