Preheat the oven to 350 degrees F (175 degrees C). Grease a 3-quart casserole dish or 13x9-inch pan.
Blend 2 cups half and half, chipotle pepper, bouillon cubes, and garlic in a blender or food processor until well-blended. Pour into a large saucepan; add onion powder, black pepper, remaining 2 cups of half and half, and corn starch. Stirring constantly, bring to a boil; boil and stir until very thick, about 1 minute. Remove from heat.
Gradually stir in 2 cups of Monterey Jack and 2 cups of pepper jack cheeses until melted. Add cooked pasta and stir until blended. Pour mixture into the prepared dish and sprinkle with remaining pepper jack.
Bake until browned and bubbly around edges, 25 to 30 minutes.
