In any CanCooker on a medium to medium low heat source cook the bacon until crispy, about 7 minutes. Using a slotted spoon transfer the bacon to a paper towel lined plate.
Drain all but about 1 – 2 tablespoons of the bacon fat from the CanCooker. Add the onion, bell pepper, jalapeno and the thyme to the bacon grease and cook until tender, about 5 minutes. Add the butter to the vegetable mixture,stirring until melted.
Sprinkle the flour over the vegetable mixture and stir until incorporated. Add the beer and stir until the mixture thickens. Add the chicken stock and whipping cream and stir until all ingredients are combined. Add the sharpcheddar, medium cheddar, and the pepper jack cheese, a handful at a time to thesoup, stirring after each addition.
When all of the cheeses have melted, season the soup with salt and pepper and add ½ of the cooked bacon. Spoon of the soup into bowls and garnish with remaining bacon, chives and parsley.