Stir together first 6 ingredients, 1/4 cup green onions, and 1/4 cup cilantro. Let stand 1 hour.
Stir together remaining green onions, remaining 1/4 cup cilantro, chicken, and diced green chiles.
Arrange 4 tortillas on a large baking sheet greased with vegetable cooking spray. Top evenly with cheese, chicken mixture, and remaining tortillas, pressing down slightly.
Bake at 425° for 8 to 10 minutes or until cheese melts. Cut into wedges, and serve immediately with salsa.
Note: Freeze remaining chipotle chiles in adobo sauce, if desired.