Cook Base
Preheat oven to 325°F.
In a large Dutch oven, cook bacon until crisp; remove and set aside, leaving fat.
Sauté onion 5–6 min. Add bell pepper, cook 3 min. Stir in garlic and jalapeños for 1 min.
Make Sauce
In a bowl, whisk sugar, ketchup, molasses, vinegar, Worcestershire, mustards, soy sauce, and spices.
Add bourbon or liquid smoke if using.
Combine & Bake
Add all beans to the pot with vegetables.
Pour in sauce, stir gently, and return bacon. Add a splash of reserved bean liquid if too thick.
Simmer on stovetop, cover, and bake 1½ hrs, stirring every 30 min.
Uncover and bake 1–1½ hrs more until sauce is thick and caramelized.
Serve
Let rest 10–15 min before serving. Garnish with extra bacon or green onions if desired.