Preheat the oven to 350°. Lightly grease two cookie sheets. Sift 3 cups flour, baking soda and cocoa together. In a separate bowl, combine the oil, vinegar, food coloring and 1/2 teaspoon vanilla.
Using an electric mixer, beat 1 1/2 cups sugar and eggs together until they turn pale and double in volume. Add the oil mixture and beat to combine. Add the flour mixture and buttermilk alternately in five small additions, starting and ending with the flour.
Drop the batter by teaspoons onto the baking sheets, allowing 1 inch between drops, as the cookies will spread. You'll be making 48 cookies. Bake until the cookies are firm but not crisp, about 12 minutes. Transfer immediately to racks to cool.
To make the filling, put the flour into a medium saucepan and slowly add the milk, whisking until smooth. Set over medium heat and cook, stirring constantly with a whisk, until very thick, about 3 minutes. Allow to cool completely.
Cream 1 cup sugar, butter, shortening and 1 teaspoon vanilla with an electric mixer. Add the cooled flour mixture and whip until fluffy. Spread onto one cookie and top it with another to make a sandwich; repeat with the remaining cookies and filling. Cover the filled whoopee pies with plastic wrap and store in the refrigerator.