Bake 18 cupcakes according to box directions. Let cool.
In a medium saucepan stir together all filling ingredients EXCEPT pecans and vanilla. Bring to a boil. Remove from heat and stir in pecans and vanilla. Pour into a bowl. Let mixture cool on the counter for 10 minutes and then refrigerate for 1 hour.
Scoop out the center of each cupcake. Fill with filling.
In a small saucepan, bring brown sugar, water, and salt to a boil. Cook for about 1 minute, stirring to dissolve sugar. Add 1/2 cup butter and stir until melted. Let mixture cool to room temperature.
Combine cooled brown sugar mixture and remaining butter in the bowl of an electric mixer. Beat until smooth.
Gradually beat in powdered sugar. Beat in milk.
Using a piping bag fitted with a large tip, frost the cupcakes.
