Preheat oven to 350°F.
Cook butter and flour over low heat for 5 minutes in large heavy bottomed saucepan, stirring frequently. Add 1/4 cup milk and whisk thoroughly so there are no lumps. Repeat. Add remainder of milk and whisk well. Bring to low boil over medium heat and lower to simmer. Add salt. Cook for seven minutes, stirring occasionally.
Add garlic and cheeses to milk. Stir until cheese is almost melted. Add lemon zest and juice, cilantro, chipotles and pasta. Stir to mix. Pour into two-quart casserole dish.
Bake for 25 to 30 minutes, until sauce starts to firm and top is golden brown and crusty. Remove from oven and cool 5 minutes before serving.