Heat olive oil in a large stock pot over medium-high heat. Add onion and pasillas and season with salt and pepper. Let cook until translucent, about 8 minutes. Add garlic and chipotles and season again. Cook another minute or two, stirring occasionally.
Add tomatoes, cumin, chicken, and water and bring to a boil. Reduce heat to a simmer and continue cooking until chicken is very tender, about 1- 1 1/2 hours. Turn the chicken from time to time so it cooks evenly.
Remove chicken from pot and set on a large plate to cool. Pour liquid through a sieve into a heat-proof bowl. Save solids, cool broth then cover and save in the refrigerator or freezer for another use.
Once chicken is cool enough to handle, shred and place in a large bowl, removing all skin and bone. Add reserved vegetables, the teaspoon of salt and squeeze the lime over the mixture. Toss together and taste to see if it needs more lime juice or salt.
Heat a cast iron skillet or nonstick frying pan over medium heat. Warm tortillas one at a time until they are very flexible, about 1 minute a side. Place in a clean dish towel to keep warm.
Place several tortillas out on a clean work surface and put about 3 tablespoons of chicken on the bottom third of each tortilla. Roll the tortilla up over the filling and continue rolling into a tight cylinder. Secure closed with a toothpick at the seam. Continue with the remaining tortillas and chicken.
Place a large, deep frying pan over medium heat. Add enough oil so it reaches 1-inch up the side of the pan. If you have a deep-fry thermometer place it in the oil, when it reaches 350°F, it is ready. If you don't have one, the oil is ready when a small cube of bread browns in 30 seconds. Meanwhile cover a baking sheet with paper towel and set near the stove.
Carefully place a few flautas at a time in the pan (they should have plenty of room to move around) and fry until brown and crisp, about 2-3 minutes. Flip and brown on the other side, about a minute more. Remove with tongs to the paper towel-lined baking sheet and repeat with remaining flautas.
Remove the toothpicks (or let your guests do this) and serve immediately with guacamole, Harissa ranch, and/or sour cream.