Drain and rinse your pre-soaked beans thoroughly under cool running water. Place them in a large Dutch oven or oven-safe pot with a tight-fitting lid.
In a large skillet over medium heat, cook the diced bacon until it begins to crisp but isn't completely done (about 5-7 minutes). Using a slotted spoon, remove half the bacon and set aside for topping later.
Add the chopped onion to the remaining bacon and drippings, cooking until translucent and starting to caramelize (about 5 minutes).
In a medium bowl, whisk together the molasses, brown sugar, maple syrup, mustard, salt, pepper, and cloves until well combined. Add the hot water and stir until sugar is dissolved. Pour this mixture over the beans in the Dutch oven.
Add the bacon-onion mixture (including the drippings) to the beans and sauce, stirring gently to combine.
Preheat your oven to 325°F (165°C). Cover the Dutch oven with its lid and bake for 4 hours, checking occasionally to ensure the beans remain moist. If they seem dry, add 1/4 cup hot water as needed.
During the last hour, remove the lid to allow the top to develop a slight caramelization.
After 4 hours of cooking, remove from the oven and stir in the apple cider vinegar.
Top with the reserved bacon pieces, return to the oven uncovered, and bake for an additional 30 minutes until the top is beautifully caramelized and the sauce has thickened.