Combine first 5 ingredients in a large Dutch oven; bring to a boil. Reduce heat; simmer 30 minutes. Strain broth; discard solids. Return broth to pan.
Place rice noodles in a large bowl; cover with hot water. Let stand 15 minutes; drain. Cook noodles in boiling water 1 minute or until tender; drain.
Combine the beef, shallots, sake, and minced ginger in a large zip-top plastic bag; seal and marinate in refrigerator 10 minutes. Add beef mixture to broth in pan; bring to a boil. Reduce heat to medium; cook 3 minutes. Stir in bean sprouts and next 6 ingredients (bean sprouts through black pepper); cook 1 minute.
Place the noodles into each of 6 large bowls; top with broth mixture. Garnish with sliced chile and lime wedges, if desired.