Preheat the oven to 350°F. Spray 18 standard muffin cups well with cooking spray.
Combine the cake mixes, eggs, vegetable oil, water, and 2 tablespoons vanilla in a large mixing bowl and mix well. Divide the batter into two equal portions. Add a few drops of red food coloring to one batch and a few drops of green to another. Stir well. Divide the red batter equally into 9 prepared muffin tins and the green into 9 muffin tins. Bake for 15-20 minutes or until a toothpick inserted into the center comes out clean. Let cool in the pans for 10 minutes, then transfer to a wire rack to finish cooling.
In the bowl of an electric mixer, preferably fitted with a paddle attachment, combine the shortening and Swerve Confectioners. Beat until fully combined, scraping down the sides of the bowl as needed. Beat in 1 tablespoon vanilla. Add milk, one tablespoon at a time, until the frosting is smooth and spreadable.
Cut the cupcakes in half horizontally. Layer into the canning jars, starting with half of one color cupcake, then a layer of frosting, a layer of the other color of cupcake, another layer of frosting, then another cupcake half, same color as the first layer. If there is room in your jar, you can finish with a layer of frosting. Repeat until all the cupcakes and frosting are used up.
Screw the tops on the jars and decorate as desired.
Gluten-Free Christmas Cupcakes in a Jar https://simplygluten-free.com/blog/2019/12/gluten-free-christmas-cupcakes-in-a-jar.html