Fill a medium pot with water, season with salt and bring to a boil. Add elbow pasta and under cook by 3 minutes less than manufacturer's directions (be sure to read the instructions on the box, each brand is slightly different).
Keep a constant eye on the pan as this will scorch easily. While whisking slowly add the warm milk. Continue cooking and whisking constantly until the mixture becomes thick and smooth; about 3-5 minutes.
Remove the pan from the heat and stir in salt, black pepper, cayenne pepper, 1-1/2 cups of sharp cheddar cheese, 3/4 cups gruyère and reserved elbow pasta. Mix well to incorporate and pour into the prepared baking dish.