Preheat the grill to medium.
Arrange the peppers on the hot grill, turning them when the skin is charred and blistered, and all sides have been roasted. Remove the peppers to a bowl and set aside to cool. Scrape the flaking skins from the chiles and dice. Grill the green onions in the same way until lightly charred and wilted. Remove them from the grill to a cutting board and finely chop. Add the chiles, onion and the shredded cheeses to a medium bowl and mix well. Put 1 tortilla on top of well seasoned comal and spread it with some of the cheese mixture. Top with some Chipotle Pico de Gallo and cover with a second tortilla. After about 2 minutes carefully flip and toast the other side, about 2 to 3 minutes. The tortillas should be golden brown and the cheese should be thoroughly melted. Repeat with remaining tortillas and filling. Cut the quesadillas into quarters for single servings or into eighths for appetizers.
Combine all the ingredients in a glass bowl and mix well. It is best to let this stand for at least 1 hour to allow the flavors to marry. Drain the salsa of excess liquid and refrigerate until ready to use.