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When ready to cook, start the Traeger grill on Smoke with the lid open until the fire is established (4 to 5 minutes). Set the temperature to 300F and preheat, lid closed, for 10 to 15 minutes.
Put a cold Dutch oven on the stovetop and add the bacon. Turn the heat to medium low and saut the bacon, stirring occasionally, until it begins to render its fat.
Add the onion and garlic and cook until translucent. Add the 6 cups of water and the beans, increase the heat to medium-high, and bring to a boil. Bury the pork shoulder and ham hock in the beans so they are covered with liquid.
Put a lid on the Dutch oven and carefully transfer it to the grill grate. Bake the beans for 2 to 3 hours, stirring occasionally. Add the barbecue sauce, applesauce, brown sugar, and mustard.
Recover the pot and continue to cook for 3 to 4 hours, stirring occasionally and adding more water if needed to keep the beans from drying out, until the beans are tender but not falling apart. (Remove the lid from the pot if the sauce needs thickening.) Retrieve the pork chunks and ham hock from the beans and shred or dice into bite-size pieces, discarding any bones, fat, skin, etc.
Stir the meat back into the pot along with the bourbon, if using, and add salt and pepper to taste. Continue to bake for a few more minutes to reheat the meat.