Mix rye flour, whole wheat flour, 1 teaspoon ground pepper, 1 teaspoon thyme, 1 teaspoon caraway seeds, garlic powder, and basil in a large resealable plastic bag. Add beef to the bag a handful at a time, tossing to coat.
Transfer beef to a large slow cooker. Add remaining 1 1/2 teaspoon thyme, 1 teaspoon caraway seeds, crushed tomatoes, onion, salt, and garlic. Pour in beer.
Cover and cook on Low for 3 to 4 hours.
Stir stew. Mix in frozen carrot mixture, green bell pepper, tomato paste, mushrooms, beef broth, gravy mix, hot sauce, and sugar.
Cover and cook on Low until beef is tender and flavors combine, about 4 hours more. Season with remaining 1 1/2 teaspoon pepper.