Place the oven rack in the middle of the oven. Preheat to 350 degrees F.
In a large pot, two-thirds full of water, bring it to boil over high heat. Salt generously. Add pasta and stir. Reduce heat to medium. Cook until pasta is al dente on the edges but still uncooked in the middle. [Use directions on box as a guide, especially if using a different kind of pasta. The cavatappi took about 9 minutes.] Strain and pour into a buttered 9x13 baking pan.
While the water is coming to a boil, heat olive oil, jalapenos and garlic in medium pan over high medium-high heat. [It definitely helps to ventilate your kitchen! Turn on an exhaust fan if you have one.] Stir frequently to ensure peppers are evenly coated with oil.
Once the peppers are lightly browned on the edges and the garlic turns golden brown, add chipotle peppers. Cook for 30 seconds, then remove from heat.
Add entire pepper mixture to blender or food processor. Use the stir or chop setting until mixture turns into a smooth sauce without lumps. [If you have trouble achieving a smooth texture, add milk about 1 TBS at a time and pulse until the sauce becomes smoother.]
Once the pasta is ready, pour the pepper sauce on top, stirring gently until evenly distributed.
To make the cream sauce, use a medium saucepan to melt the butter over medium heat. Add flour and stir until a grainy, yellowish paste is created.
Add milk to the roux and stir constantly for several minutes until the sauce noticeably begins to thicken. Add cheddar cheese and stir until melted. Stir in 2 teaspoons salt.
Pour the cream sauce onto the pasta-peppers mixture and stir gently until it is evenly distributed.
10. Cover the baking pan with aluminum foil, shiny side down. Place in the center of the oven and bake for 20 minutes.
11. Remove the foil and bake uncovered for 10 minutes. Remove from the oven. Let stand for 5 minutes. Serve.