Sift together the whole wheat flour, pastry flour, baking powder and salt, set aside.
In a medium bowl, stir together the vegetable oil, 2 cups of peanut butter, honey and yogurt until smooth.
Add the dry ingredients and mix by hand until well blended.
Shape into a roll that is 2 inches in diameter, wrap and chill until firm.
Preheat oven to 350 degrees F (175 degrees C).
Unwrap the roll of dough, and slice into 1/4 inch slices.
Place half of the cookies onto unprepared baking sheets.
Spread 1/2 teaspoon of peanut butter onto the center of each cookie on the sheets, cover with the remaining cookie rounds, and seal edges tightly with a fork.
Bake for 10 to 12 minutes in the preheated oven.
Remove cookies from baking sheets to cool on wire racks.