Add water to a large pot and bring to a boil. Add elbow pasta to the pot of boiling water, and add 1 teaspoon salt. Set a timer for 7 minutes. Cook the pasta until al dente (not completely soft and tender).
Meanwhile, using a 10" cast-iron skillet, fry the bacon until crispy then drain on paper towels. Add minced garlic and fry for approximately 30 seconds. Sprinkle flour into the pan to make a roux. Stir over low heat for about a minute then turn off the heat.
Drain cooked pasta and add to a medium-sized bowl. Pour milk over the pasta, then add cream cheese, salt, and pepper. Shred cheddar and gouda and add, along with bacon.
Stir in the diced chipotle peppers and their sauce into the pasta, then pour the contents of the bowl into the cast iron pan. Mix with a rubber spatula to incorporate the garlic and roux that are in the pan into the pasta.
Cover the skillet with a lid or foil and simmer over low heat for 5 minutes. Stir pasta and place uncovered on the grill. Smoke for 30 minutes (not you, the pasta). Stir once more and sprinkle with the Colby jack cheese. Smoke, uncovered, for an additional 30 minutes.
Optional: Sprinkle the finished Smoked Mac and cheese with crispy jalapeños before serving.