1. Position a rack in the center of the oven and preheat to 350 F. Lightly spray twelve 2-3/4 x 1-1/2-inch nonstick muffin cups with oil.
2. In a medium bowl, whisk the flour, cinnamon, baking soda, and salt until well combined. Set aside.
3. In another medium bowl, using a handheld electric mixer set at high speed, beat the applesauce, sugar, egg, and lemon juice and zest until frothy, about 2 minutes. Make a well in the center of the dry ingredients and pour in the applesauce mixture. Using a spoon, mix just until moistened (there should be a few traces of flour remaining). Gently fold in the berries until the flour is incorporated. Do not over mix.
4. Divide the batter equally among the prepared muffin cups. Bake until the tops spring back when pressed gently in the center, about 20 minutes. Do not over bake. Cool in the pan on a wire cake rack for 10 minutes before removing from the cups. Serve warm or cool completely on the rack.
5. For Lemon Custard: Put 1 tablespoon of vanilla into a large mixing bowl with corn starch. Slowly whisk in egg yolks then add whole eggs and whisk to combine. Meanwhile, place remaining vanilla, milk, cream cheese, and lemon juice and zest in a saucepan. Bring to a simmer and cook gently for 5 minutes. (do not allow to boil) Gently pour milk mixture into the bowl containing eggs, whisking all the while, until all the milk mixture has been combined.
6. Pour the custard back into the saucepan and return to heat. Cook, whisking constantly, until the custard has thickened and is just about to bubble. Remove from heat and place on clean bowl.
7. Chill for 1 hour, until completely set and cold. Serve in 2 tablespoon size scoop with each muffin.