Combine cumin, chili powder, garlic powder, smoked paprika, salt, and pepper. Rub evenly over both sides of the chicken thighs.
Heat 1 tbsp olive oil in a large skillet over medium-high heat until shimmering. Cook chicken 7 minutes per side, undisturbed, until the internal temperature reaches 75°C (165°F). Transfer to a cutting board and rest 5 minutes. Shred with two forks.
In the same skillet over medium heat, add 1 tsp olive oil and sauté the diced onion for 4 minutes until translucent. Add garlic, cook 1 minute more.
Add shredded chicken to the skillet. Pour in 1/2 cup (120ml) enchilada sauce. Stir to combine and remove from heat.
Preheat oven to 190°C (375°F). Spread 1/2 cup (120ml) enchilada sauce across the bottom of a 23x33cm (9x13 inch) baking dish.
Warm each corn tortilla in a dry skillet for 20-30 seconds per side. Keep wrapped in a kitchen towel.
Fill each tortilla with 2 heaped tablespoons of chicken filling and a small pinch of Monterey Jack. Roll tightly and place seam-side down in the baking dish.
Pour remaining 1.5 cups (360ml) enchilada sauce over the rolls, covering all exposed tortilla. Top with remaining Monterey Jack and all of the cheddar.
Bake uncovered at 190°C (375°F) for 20-25 minutes until cheese is fully melted, bubbling, and golden in patches.
Rest 5 minutes. Garnish with cilantro, green onions, and jalapeño slices. Serve with sour cream.