Start by preheating oven to 350 degrees and spraying a 9x13 baking pan with nonstick spray. Bring a large pot of salted water to boil. Cook shells following box instructions but pull 1 minute early. Drain and set aside to cool slightly.
While pasta is cooking, make your jalapeno cheese sauce. Add diced jalapeno pepper to a large skillet and heat over medium high heat for 1-2 minutes. Add minced garlic and stir to cook for 1 minute. Move 2/3 of the jalapeno and garlic to a large mixing bowl while leaving the remaining amount in your skillet.
To your skillet, add in your butter and once your butter is melted, add in the flour.Whisk together and continue whisking while your flour cooks for 1-2 minutes before slowly pouring in the milk and chicken stock. Whisk together to combine and break up any flour clumps.Add in salt and pepper and bring to a low boil, stirring often. Once boiling, turn heat down to medium and stir in the Parmesan cheese and Pepper Jack cheese and continue to stir until all of your cheese has melted.
In a large bowl, combine bacon, 2 diced jalapeno peppers, shredded rotisserie chicken, cream cheese, sour cream, green onions and 1/2 cup shredded cheese. Spoon jalapeno popper mixture into the shells and place open sides up in the baking pan. Cover with jalapeno cheese sauce and sprinkle with remaining cheddar cheese. Bake for 20-25 minutes. Remove and serve immediately.