Bring a large pot of salted water over high heat to a boil. Add pasta shells, and cook according to package directions until al dente. Drain, rinse with cold water and reserve pasta.
In a large pot, whisk together evaporated milk and chipotle puree over medium-high heat. Bring just to a boil, immediately removing from heat upon boiling. Add 3 tablespoons melted butter, eggs, mustard, salt and pepper, and whisk together.
Add the reserved pasta and cheeses. Over low heat, stir slowly for 1 to 2 minutes until cheese has melted and is incorporated with the pasta. Finish with remaining 1 tablespoon of butter. Serve.