Heat 1 tablespoon butter in a large (12-inch) cast iron skillet. Add shallot; cook until softened, 3-5 minutes. Add remaining butter and flour; cook 2 minutes, stirring constantly. Stir in stock, scraping the bottom of pan. Add pumpkin, chipotle and adobo; cook over medium-high until mixture begins to bubble, about 2 minutes. Reduce heat to low; add 1 cup each goat cheese and Manchego and stir until cheese melts, 1 minute. Remove from heat; stir in chopped jalapeños and jalapeño juice.