Preheat your oven to 350°F. This takes 10–15 minutes. Line a jumbo muffin tin with paper liners or grease the cups with butter or cooking spray. The tin should have 6 cups. Set aside.
In a large mixing bowl, whisk together 2 cups all-purpose flour, 1 teaspoon baking soda, 1 teaspoon baking powder, and 1/2 teaspoon salt. Mix for 30 seconds. This removes lumps and distributes leavening agents evenly.
Add 2 teaspoons ground cinnamon, 1/2 teaspoon ground nutmeg, 1/4 teaspoon ground ginger, and 1/4 teaspoon ground cloves to the dry mixture. Stir for 20 seconds until the spices are evenly distributed. The mixture should smell warm and aromatic.
In a separate medium bowl, whisk together 3/4 cup vegetable oil and 1 cup granulated sugar. Whisk for 1–2 minutes until the mixture is pale and slightly frothy. This helps incorporate air.
Add 3 large eggs one at a time to the oil-sugar mixture, whisking well after each addition. This takes about 2–3 minutes total. The mixture should be smooth and pale yellow.
Stir 1 teaspoon vanilla extract into the wet mixture. Mix for 10 seconds.
Pour the wet ingredients into the dry ingredients. Using a silicone spatula or wooden spoon, fold together gently for about 1 minute, stirring only until no dry flour streaks remain. Do NOT overmix or the muffins will be tough. The batter should be thick and chunky-looking.
Fold in 2 cups finely grated carrots (about 3–4 medium carrots; use the large holes on a box grater or a food processor). Fold for 20–30 seconds until evenly distributed.
Add 1/2 cup unsweetened applesauce and fold for 15 seconds until combined. The batter will be thick and moist.
Fold in 1/2 cup crushed pineapple with its juice. Fold for 20 seconds until the liquid is absorbed. The batter should now be quite moist but still hold its shape.
Gently fold in 1/2 cup chopped walnuts or pecans and 1/3 cup raisins (or dried cranberries) for 20–30 seconds until evenly distributed. Set batter aside.
Spoon the muffin batter into your prepared jumbo muffin cups, filling each about three-quarters full (roughly 1/3 cup batter per cup). The batter should be slightly mounded above the rim. This takes about 2 minutes.
Place the muffin tin on the center oven rack. Bake for 28–32 minutes. The muffins are done when the tops are golden brown and spring back lightly when touched. A toothpick inserted into the center should come out clean or with just a few moist crumbs. The kitchen will smell fragrant and spiced.
Checkpoint: Muffins are ready to cool when the tops are golden, the sides have pulled slightly from the tin, and a toothpick emerges clean.
Remove the muffin tin from the oven and place it on a wire cooling rack. Let the muffins rest in the tin for 10 minutes. This helps them firm up so they don't fall apart when you remove them.
After 10 minutes, carefully run a thin knife around each muffin to loosen it from the cup. Gently lift each muffin out by the paper liner and place on a wire rack. Let cool for at least 30 minutes before frosting or serving.
While muffins cool, prepare the optional cream cheese frosting. In a medium bowl, beat 8 ounces softened cream cheese and 1/4 cup softened butter together with an electric mixer on medium speed for 2–3 minutes. The mixture should be light, fluffy, and pale yellow. This incorporates air and makes the frosting fluffier.
Gradually add 2 cups powdered sugar to the cream cheese mixture in three additions. After each addition, beat for about 20–30 seconds. Beat on low speed first to prevent sugar from flying everywhere, then increase to medium speed. Scrape down the bowl with a spatula between additions.
Stir in 1 teaspoon vanilla extract and beat for 10–15 seconds until the frosting is smooth and spreadable. The frosting should be thick but not stiff. If it's too soft, refrigerate for 15 minutes. If it's too stiff, add 1 tablespoon milk at a time and stir.
Once muffins are completely cool (at least 30 minutes), spread or pipe a generous dollop (about 2–3 tablespoons) of cream cheese frosting on top of each muffin. Alternatively, drizzle a light coating of frosting over each. Let the frosting set for 10 minutes at room temperature or 20 minutes in the refrigerator.
Checkpoint: Frosted muffins are ready to serve when the frosting is set and no longer slides off the muffin tops.