Preheat oven to 250°F.
In a small ungreased skillet over high heat, toast fennel seeds, stirring constantly, for one to two minutes or until they are fragrant. Remove from pan, allow to cool, and place at the center of a coffee filter. Tie filter closed with kitchen twine.
In a large, oven-safe pot on stove, cook bacon over low heat until fat has rendered out into pot and bacon is crispy and brown. Remove bacon to paper towel-lined plate, leaving fat in pot. Raise temperature to medium.
Season shanks with salt and pepper, roll them in flour, and shake off excess. Brown on all sides in bacon fat. Remove shanks and add onion, celery, carrots, and garlic. Reduce heat to medium-low and cook for about five minutes. Add red wine and reduce by half, about four minutes. Add rest of ingredients (including fennel package) and shanks.
Cover pot and place in oven for about three and a half hours. Using a fork, check to see if meat peels from bone easily. If still attached, continue to cook until meat falls off bone. Let meat cool in liquid for about 10 minutes. Use a ladle to skim fat off top of braising liquid and discard. Serve immediately or refrigerate for up to three days.
When ready to serve, place warm meat on a platter. Season liquid with salt and pepper. Discard fennel seeds and bay leaves. Sauce meat with braising liquid.