Preheat the oven to 400°F.
For the cheese sauce, heat a medium-size sauce pan over medium heat. Add the butter to melt. Add the flour and stir until bubbly, about 2 minutes. Slowly whisk in the milk; keep whisking until the mixture starts to thicken, about 3 minutes. Whisk in the cheeses and sour cream until smooth. Stir in the chipotle pepper (or hot sauce), cumin, paprika, salt and pepper. Remove from heat until ready to serve. If sauce is lumpy, place into a blender and blend until smooth.
For the nachos, mix the chicken and salsa together in a medium bowl. Place the chips on a foil-lined sheet tray. Top the chips with half the cheese, all of the chicken and then top the chicken with another layer of cheese.
Place the sheet tray into the oven and bake for 8-10 minutes or until cheese is melted and chicken is warmed through.
While the nachos are in the oven, warm the cheese sauce over a medium low heat.
Once the cheese has melted on top of the chicken, remove from oven and top with all of the warm cheese sauce and garnish with red onion, jalapeño, radish and cilantro.