Cook bacon in large skillet over medium-high heat until crisp. Using slotted spoon, transfer bacon to paper towel-lined plate and refrigerate. Pour half of bacon fat into small bowl; set skillet with remaining bacon fat aside.
Dry beef thoroughly with paper towels. Season beef with salt and pepper; place half of beef in slow cooker insert. Heat skillet containing remaining bacon fat over medium-high heat until just smoking. Cook remaining beef in single layer until deep brown on all sides, about 8 minutes. Transfer browned beef to slow cooker insert.
Add reserved bacon fat to now-empty skillet and heat over medium-high heat until shimmering. Add onion, carrots, and 1/4 teaspoon salt and cook until vegetables begin to brown, about 5 minutes. Add garlic and thyme and cook until fragrant, about 30 seconds. Add tomato paste and stir until beginning to brown, about 45 seconds. Transfer mixture to slow cooker insert.
Return now-empty skillet to high heat and add 1 1/2 cups wine, chicken broth, and soy sauce. Simmer, scraping up brown bits, until pan bottom is clean, about 1 minute. Transfer wine mixture to slow cooker insert.
Stir bay leaves and tapioca into slow cooker insert. Set slow cooker on low, cover, and cook until meat is fork-tender, about 9 hours.
When ready to serve, discard bay leaves and stir in reserved bacon. Bring remaining 1 cup wine to boil in large skillet over high heat and simmer until reduced by half, about 5 minutes. Stir reduced wine and parsley into stew and adjust seasonings. Serve with sauteed onions and mushrooms on top.