Make the pickled red onion: Combine the cider vinegar, sugar and 1 teaspoon salt in a medium bowl and whisk to dissolve. Add the red onion and 2 tablespoons cilantro and stir to combine. Cover and set aside at room temperature, 1 hour.
Meanwhile, soak 20 wooden skewers in warm water, at least 20 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, the garlic, red wine vinegar, lemon juice, red pepper flakes, 1/2 teaspoon 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. 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 and pickled onion.