Preheat oven to 350°.
Place bread in a food processor; pulse 2 times or until crumbly. Sprinkle crumbs on a baking sheet; bake at 350° for 5 minutes or until golden.
Increase oven temperature to 400°.
Heat a large nonstick skillet over medium-high heat. Coat pan with cooking spray. Add green onions and onion to pan; sauté 5 minutes. Add mushrooms to pan; sauté 3 minutes or until mushrooms soften and most of liquid evaporates. Add chopped thyme; cook 30 seconds. Remove from heat. Combine mushroom mixture, breadcrumbs, and bacon in a bowl.
Open trout flat as you would a book. Drizzle trout evenly with juice; sprinkle evenly with salt and pepper. Spoon about 1/4 cup mushroom mixture onto bottom half of each fish; fold over to cover with top half of fish. Arrange fish on a foil-lined broiler pan. Bake at 400° for 15 minutes or until fish flakes easily with a fork or until desired degree or doneness. Garnish with lemon wedges and thyme sprigs, if desired. Serve immediately.