In large resealable food-storage plastic bag, mix lime peel, lime juice, garlic, cilantro, red pepper flakes and 1 tablespoon of the oil. Add pork; seal bag and turn to coat with lime mixture. Refrigerate 30 minutes to 2 hours to marinate.
In 12-inch nonstick skillet, heat 1 tablespoon of the oil over medium heat. Add onions; cook 7 to 10 minutes, stirring frequently, until onions turn golden brown. Remove onions from skillet; keep warm.
Heat oven to 375°F. Remove pork from marinade; drain pork on paper towels to remove excess moisture. Discard marinade.
In same skillet, heat 1 tablespoon of the oil over medium-high heat. Add pork; cook 5 to 7 minutes, stirring occasionally, until no longer pink in center. Remove skillet from heat; set aside.
Brush 1 tablespoon oil on bottom and sides of 13x9-inch (3-quart) glass baking dish or 2 (8-inch square) glass baking dishes. In medium microwavable bowl, place refried beans. Cover with microwavable paper towel; microwave on High about 1 minute or until warm.
To assemble, spoon 2 tablespoons beans down center of each tortilla. Top with pork, onions and cheese. Roll up tortillas; place seam sides down in baking dish. Lightly brush remaining 1 tablespoon oil over tortillas.
Bake uncovered 18 to 24 minutes or until edges of tortillas are golden brown. Serve with salsa and sour cream.