For the nachos, marinate the beef: In a large mixing bowl, combine the oil, onion, garlic, thyme, vinegar, onion powder, garlic powder, cayenne and red pepper flakes. Add the beef, cover and refrigerate for at least 6 hours or up to 3 days.
For the pico de gallo, in a medium bowl, combine all the ingredients and mix well. Season to taste with salt.
For the guacamole, in a medium bowl, combine all the ingredients and mix well.
Prepare a two-stage grill with high and medium-low sides. Season the beef with salt and pepper, place on the hot side of the grill and sear, turning once, until charred on both sides, about 3 minutes a side. Move the meat to the medium-low side of the grill and continue grilling, turning the meat over every 10 minutes or so, until an instant-read thermometer inserted in the thickest part of the meat reaches 140°F for medium, about 35 to 40 minutes total. Transfer the meat to a cutting board and let rest for 15 minutes before cutting into ½-inch dice. (You will have leftover beef; start by cutting about 2 cups’ worth and reserve the rest for another use.)
Working in batches, arrange the chips on an oven-safe baking dish or a microwave safe plate. Top each chip with half a slice each of cheddar and Monterey Jack. Microwave the nachos at full power just until the cheese melts, 30 to 45 seconds. Top each chip with a piece or two of beef, a dollop each of guacamole and sour cream and a spoonful of pico de gallo. Repeat with the remaining ingredients and serve.