Preheat oven to 350 degrees. Coat a 2 quart baking dish with cooking spray.
Melt butter in a sauté pan. Add Andouille sausage and sauté for 2 minutes. Add onion, red bell pepper, and crawfish. Saute 2 minutes and remove from heat.
Place cooked pasta in a large bowl. Whisk together eggs and milk and pour in bowl with pasta.
Add spices and salt to pasta bowl along with crawfish mixture.
Mix cheeses in a medium bowl and set aside 1/2 cup of cheese. Add the rest of the cheese to the pasta. Mix together well and pour into prepared dish.
Sprinkle cracker crumbs and reserved 1/2 cup cheese on top.
Cover dish with aluminum foil and bake 15 minutes. Remove foil and bake uncovered for 5 minutes.