Preheat the oven to 400° F. Pierce the sweet potatoes with a fork and place on a parchment-lined rimmed baking sheet. Bake until completely soft, about 55-60 minutes. Remove from the oven. Reduce oven temperature to 325°F. Line standard muffin tins with paper liners.
When cool enough to handle, slice each potato in half and scoop the flesh into a large bowl; discard the skins. Mash with a fork until smooth and set aside. You should have about 1¾ cups.
In a medium bowl, whisk together flour, starch, baking powder, baking soda, salt, and spices; set aside.
Add sugar, maple syrup, eggs, butter, orange juice, and zest to the sweet potato flesh and mix until smooth. Add the flour mixture and mix until fully incorporated. Divide batter evenly among prepared muffin tins, filling each three-quarters full.
Bake for 18-20 minutes or until a toothpick inserted into the center comes out clean. Cool completely in the pans on wire racks before removing cupcakes.
To make the frosting, beat the cream cheese and butter in a medium bowl with an electric mixer on medium-high speed until creamy, 2-3 minutes. Reduce speed to low and gradually beat in powdered sugar until well blended. Beat in salt and vanilla. Spread the frosting on top of each cupcake with a spoon. Sprinkle with graham cracker crumbs.