In a large Dutch oven, sauté chopped onion over medium-high heat for 3 minutes. Add 2 chopped jalapeños and cook for 2 more minutes, then add garlic, chili powder, cumin, salt & pepper. Cook for another 30 seconds.
Stir in flour and cook for 2 minutes.
Add chopped squash, chicken stock, and milk. Bring to a boil, partially cover with a lid, and cook at a simmer for 8 minutes.
Add 2 cups of corn and cook for 5 minutes.
Reduce heat to low. Using an immersion blender, thoroughly blend the vegetables until they are finely pureed. (*NOTE: you can also use a food processor or blender to process the chowder, however use extreme caution pouring the hot liquid and be sure to allow steam to escape from the top of the blender/processor by removing the small top cover and draping it with a kitchen towel)
Raise heat back to medium, then add the chopped potatoes and cook about 10 minutes.
Add 2 more cups of fresh uncooked corn, and cook for another 5 minutes.
Stir in Monterey Jack cheese, until melted. Fold in the shredded chicken and allow the chowder to cook for 2-3 more minutes to heat the chicken and combine into the chowder.
Serve while hot, and top with chorizo, shredded cheddar cheese, chopped jalapeño, cilantro, & green onions.