In a two cup measuring cup, combine beer, soy sauce, lime juice, oil, Worcestershire sauce, garlic, and red pepper flakes. Place chicken in a large resealable bag. Add 3/4 cup beer mixture. Reserve remaining beer mixture. Marinate in refrigerator for 1 hour, turning occasionally.
In a large resealable bag, combine onion, bell peppers, and remaining beer mixture. Marinate for 1 hour at room temperature.
Heat a grill pan over medium-high heat. Spray pan with cooking spray. Remove chicken from bag and discard marinade. Sprinkle chicken evenly with salt and black pepper. Add chicken to pan and cook until no longer pink, about 2 minutes on each side. Remove chicken from pan and keep warm. Remove onion and bell peppers from bag and discard marinade. Add onion mixture to pan and cook for 6 minutes or until tender, turning after 3 minutes. Toast tortillas in pan.
Divide chicken and onion mixture evenly among tortillas. Garnish with jalapeño slices. Serve with salsa, sour cream, guacamole and cilantro, if desired.