Preheat oven to 350 degF. Coat a 3-quart baking dish with cooking spray.

Place english muffin pieces on a large rimmed baking sheet. Bake until lightly toasted, about 10 minutes.

Combine apples, 1/2 cup raisins and cinnamon in a large bowl. Add the english muffin pieces and toss to combine. Transfer to the prepared baking dish, spreading into a single layer and redistributing any raisins that fall to the bottom.

Whisk eggs, milk, pumpkin, brown sugar, salt, ginger, and cloves in a medium bowl until smooth. Pour over the bread mixture and press down so everything is submerged. Sprinkle the remaining 1/4 cup raisins over the top. Cover with plastic wrap, pressing it down so it’s directly on the surface. Refrigerate for least 1 hour or up to 12 hours.

Bake the casserole at 350 degF until browned and a little crispy around the edges, but still creamy in the middle, 50 minutes to 1 hour. Let cool slightly before serving.