In a heavy-bottomed pot, cook bacon over medium heat until browned but not crispy, about 15 minutes.
Transfer bacon to a paper towel-lined plate.
Cool for 5-10 minutes and then pour off all but about 1/2 tablespoon of bacon fat into a heat-proof container.
Add diced onion and cook on medium heat until soft and translucent, about 5-6 minutes.
Stir in bourbon, vinegar, water, molasses, and brown sugar. Bring to a boil, scraping up any browned bits.
Add chocolate and cooked bacon. Stir until melted and combined.
Reduce heat to low and simmer for 2 hours, stirring every 20-30 minutes, until most of the liquid is gone.
Use an immersion blender to blend until mostly smooth but with some texture remaining.
Cool completely, then refrigerate. Remove and discard the solidified fat from the top, if present.
Make the Dough
Cream butter, brown sugar, and honey until smooth.
Add egg and vanilla and mix until fully incorporated.
In a separate bowl, whisk together flours, baking soda, salt, and cinnamon.
Add dry ingredients to wet ingredients and mix just until combined.
Add milk, adjusting as needed, until dough is soft and pliable but not sticky.
Wrap and chill for at least 1 hour.
Assemble and Bake
Preheat oven to 350 F and line baking sheets with parchment.
Roll dough on a floured surface into rectangles about 1/4 inch thick.
Cut out pig shapes with a cookie cutter or cut into rectangles.
Re-roll scraps and cut out again. Continue until all the dough is used. (Chill again if the dough becomes too sticky to work with.)
Place half of the pigs onto baking sheets leaving 2 inches of space between pigs.
Spread bacon jam on half of the pigs, about 1/2 inch thick.
Place the remaining pigs on top of the pigs with the jam and press down lightly.
Bake for 12-15 minutes, until set and lightly golden. Swap trays in the oven halfway through for even baking.
Set cookies on a cooling rack to come to room temperature.
Video
Notes
You will have leftover bacon jam. Use it as a spread on bread or crackers or mixed into vanilla ice cream.
The filling should be thick, not runny. If it spreads, cook it down more.
Cookies will soften and improve in texture after sitting for several hours or overnight.
Store at room temperature in an airtight container for up to 48 hours. Then, move to the fridge for up to a week - bring to room temperature before serving.