Cook the bacon in a small dutch oven or heavy-bottomed stock pot over medium heat until brown, but not yet crispy. It will release lots of grease.
Remove the cooked bacon from the pot and set aside on top of paper towels to absorb excess grease.
Pour off all but approximately 1 tablespoon of the grease from the pot and discard.
Add onions to the pot with the remaining bacon grease and cook until translucent, about 6 minutes.
Add in bourbon, vinegar, water, molasses, and brown sugar, and bring to a boil, scraping down the sides to release browned bits.
Add in the chocolate and cooked bacon, and stir to combine.
Reduce heat to a low simmer. Cook for two hours, stirring every 20-30 minutes. You're halfway done!
Use a hand blender or food processor to puree the jam until you reach a smooth texture that still has some bacon bits remaining. You don't want a puree.
Continue to simmer on low heat for another 2 hours, stirring every 20-30 minutes, until jam has reduced to a thicker consistency. When you're done, the jam will resemble a thick, meaty pasta sauce. It will get much thicker after it cools.
When the jam reaches room temperature, refrigerate it for a few hours.
A large quantity of the grease will rise to the top of the bacon jam and congeal in the fridge. Unless you are a glutton for grease, scrape it all off and discard it.
Warm the jam in the microwave right before serving.
My best guess (I haven't tested it) is that bacon jam would last for a week in the refrigerator. I'd freeze it if I wanted it to last longer than that.