In a bowl, mix cumin, chili powder, and 1 teaspoon salt. Brush tortillas lightly on both sides with 2 tablespoons oil; sprinkle spice mixture on both sides of tortillas. Stack tortillas and cut into eight wedges. Arrange wedges in single layers on two 12- by 15-inch baking sheets. Bake in a 375° oven, switching pan positions midway through baking time, until crisp all over and browned at edges, 10 to 15 minutes. Let cool; store airtight until serving, up to 3 days.
Pour tablespoon oil into a 5- to 6-quart pan over medium-high heat; when hot, add yellow onions and garlic. Cook, stirring occasionally, until onion is limp, about 8 minutes. Add broth and bring to a boil. Reduce heat to maintain a simmer, cover, and cook to blend flavors, 10 minutes.
Remove pan from heat and let broth cool to room temperature. Pour broth through a fine strainer into a large bowl or soup tureen. Discard onion. Stir in the lime juice and chipotle purée and salt to taste. Cover and chill until cold, at least 2 hours, or up to 1 day.
In a bowl, mix tomatoes, red onion, and cilantro.
To serve soup, stir tomato mixture into broth. Place lime wedges, queso fresco, and tortilla chips in separate bowls. Set out bowls for guests to ladle soup into, then top with garnishes.
To make chipotle chile purée, whirl the contents of a 7-ounce can of chipotle chiles (including sauce) in a blender or food processor until smooth. Scrape into a plastic container and store airtight in the refrigerator for up to 3 weeks.