Make the pickled onion by combining the cider vinegar, sugar, and 1 tsp. salt in a medium bowl and whisk to dissolve. Add the red onion and 2 tbsp. cilantro - stir to combine. Cover and set aside at room temperature for 1 hour.
Meanwhile, soak 20 wooden skewers in warm water, at least 30 minutes. Slice the flank steak against the grain into 20 strips, about 1/8 inch thick. Thread the meat accordion-style onto the skewers and set aside until ready to grill.
Combine the remaining cilantro, garlic red wine vinegar, lemon juice, red pepper flakes, 1/2 tsp. salt and the olive oil in a blender and puree until smooth. Transfer to a small bowl.
Heat a grill or grill pan to medium high heat. Season the steak with salt and pepper. Brush the grill with olive oil, then grill the skewers until marked, about 1 minute per side. Serve with the chimichurri sauce and the pickled onion.