Adjust the oven rack to the lower-middle position and preheat the oven to 325 degrees F.
Fry the regular chopped bacon in a large, deep skillet until the bacon has partially cooked and released about 1/4 cup drippings. Add the onions, peppers and jalapenos, and saute until tender, about 5 minutes. Add the beans, barbecue sauce, brown sugar, vinegar, ketchup, mustard and chipotles, and bring to a simmer. (If the skillet is not large enough, add the beans and heat to a simmer and then transfer to a large bowl and stir in the remaining ingredients). Pour the flavored beans into an aluminum pan. Top with the uncooked slices of bacon (you can halve the slices if you like). Then bake until the beans are bubbly and the sauce is the consistency of pancake syrup, about 2 hours. Let stand to thicken slightly and serve.
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