First prepare the jalapeños. Bring vinegar, salt and sugar to boil in a small sauce pot. Pour over jalapeños. Cover and let sit as you prepare the chicken. This can also be made days in advance! They just get better with time :)
For the chicken, in a large pot, heat oil over medium heat. Season chicken all over with salt. Place in hot pot, skin side down and cook until skin is golden brown.
Flip and cook second side until lightly golden.
Remove chicken from pot and set aside. Add onion, tomatoes, tomatillos, and garlic and cook until they are charred and slightly softened.
Add in chicken stock, chipotles, oregano, and bay leaves. Return chicken to pot. Reduce heat to low. Cover and cook until chicken is cooked through, about 25-35 minutes.
Once chicken is cooked remove to a bowl and set aside.
Remove bay leaves from pot. Blend all ingredients in pot until smooth. Reduce sauce until thick, about 10 minutes. Season with salt to taste.
Remove skin and bones from the chicken and shred with two forks. Return chicken to sauce.
Serve shredded chicken in warmed corn tortillas topped with onion, cilantro, queso fresco, pickled jalapeños, and lime wedges on the side.