Whisk together flours, wheat germ, cinnamon, baking soda, and salt.
Beat butter and sugar with a mixer on medium speed until pale and fluffy, about 2 minutes. Beat in honey. Scrape down sides of bowl. Add flour mixture, and beat until combined.
Turn out dough, and divide in half. Shape dough into 2 balls. Wrap each in plastic, and refrigerate for 20 minutes. Roll out each ball into a rectangle (1/8- to 1/4-inch thick) on a floured piece of parchment. Refrigerate until firm, about 30 minutes.
Preheat oven to 350 degrees. Using a fluted pie cutter, mark 24 rectangles (each 1 1/2 by 2 3/4 inches) on each dough sheet, scoring but not cutting all the way through. Prick dough with a fork to create dotted lines. Freeze until firm, about 30 minutes.
Transfer dough on parchment to baking sheets. Bake until golden brown, 17 to 19 minutes. Let cool on sheet. Break cookies at perforations.
Transfer chocolate to a resealable plastic bag. Cut a tiny opening in 1 corner. Transfer half the cookies to a wire rack, and drizzle with chocolate. Refrigerate until set, about 20 minutes. Spread 1 teaspoon jam on underside of each remaining cookie; top with decorated cookies.
Cookies without chocolate and jam can be stored at room temperature for up to 1 week; otherwise, 2 days.