In a medium saucepan over medium heat, combine the frozen cherries, orange juice, and maple syrup. Stir occasionally until the cherries are heated through and begin to break down, about 5-7 minutes. Remove from heat and set aside.
In a large mixing bowl, whisk together the eggs, low-fat milk, Yoplait cherry orchard yogurt, vanilla bean paste, almond extract, and kosher salt until well combined.
Cut the whole grain bread into cubes and add them to the egg mixture. Gently fold the bread into the mixture until all the cubes are well coated. Let it sit for about 10 minutes to absorb the flavors.
Preheat your oven to 350°F (175°C). Grease a muffin tin lightly. Spoon a layer of the cherry filling into the bottom of each muffin cup, followed by a generous scoop of the egg-soaked bread mixture. Top each cup with a sprinkle of sliced almonds for an added crunch.
Place the muffin tin in the preheated oven and bake for 20-25 minutes or until the cups are golden brown and set in the middle.
Once baked, let the cups cool in the muffin tin for about 5 minutes. Carefully remove them and serve warm. You can top them with additional yogurt or fresh cherries if desired.