To prepare brisket, combine the first 5 ingredients. Place 2 tablespoons sugar mixture in a blender. Set aside remaining sugar mixture.
Remove 2 chiles and 2 tablespoons sauce from can; add to blender. Reserve remaining chiles and sauce for another use. Add 1 cup chopped onion and next 3 ingredients (through beer) to blender; process until smooth. Combine brisket and chipotle mixture in a 2-gallon zip-top plastic bag; seal. Marinate in refrigerator 24 hours, turning occasionally.
Soak wood chunks in water about 16 hours; drain. Remove brisket from bag, discarding marinade. Pat brisket dry, and rub with remaining sugar mixture. Let brisket stand at room temperature for 30 minutes.
Remove grill rack; set aside. Prepare grill for indirect grilling, heating one side to medium-low and leaving one side with no heat. Maintain temperature at 225°.
Pierce bottom of a disposable aluminum foil pan several times with the tip of a knife. Place pan on heated side of grill; add half of wood chunks to pan. Place another disposable aluminum foil pan (do not pierce pan) on unheated side of grill. Pour 2 cups water in pan. Coat grill rack with cooking spray, and place on grill.
Place brisket on grill rack over foil pan on unheated side. Close lid; cook 3 1/2 hours or until a meat thermometer registers 170°. Add additional wood chunks halfway during cooking time.
Preheat oven to 250°.
Remove brisket from grill. Place sliced onion and jalapeño on a large sheet of aluminum foil. Top with brisket; seal tightly. Place foil-wrapped brisket in a large baking pan. Bake at 250° for 1 1/2 hours or until thermometer registers 190°. Remove from oven. Let stand, still wrapped, 1 hour. Unwrap brisket, reserving juices; trim and discard fat. Cut brisket across grain into thin slices.
To prepare sauce, finely chop sliced onion and jalapeño; set aside. Place brisket juices in a zip-top plastic bag inside a 2-cup glass measure; let stand 10 minutes (fat will rise to the top). Seal bag; carefully snip off 1 bottom corner of bag. Drain 1/2 cup drippings into a saucepan, stopping before fat layer reaches opening; discard fat and remaining drippings. Add onion, jalapeño, broth, and remaining ingredients to pan; cook over medium heat 5 minutes or until thoroughly heated.
Beer note: Smoky brisket calls for a smoky beer. Although the Lone Star State makes some excellent brews (any of which would pair well with Texas barbecue), try Germany's Aecht Schlenkerla Maerzen beer, which has an alluring aroma of bacon and smoked sausage from the use of smoked barley. Its full body and gentle malt sweetness balance the spicy sauce. At 16.9 ounces, one bottle ($4) is enough to share. --Jeffery Lindenmuth