Preheat oven to 400°F. Cut stems off tomatoes. Roast on a rimmed sheet pan until soft, 35 - 40 minutes. Leave oven on.
While tomatoes roast, heat 2 tablespoon oil in skillet over medium-high heat. Once pan is hot, add chicken breasts and cook 4 - 5 minutes per side until golden brown. Total 8 - 10 minutes or until chicken reaches internal temperature of 165°F. Remove from pan, cool slightly and use two forks to shred chicken. Set aside.
Heat 1 tablespoon oil in same large skillet over medium-high heat. Saute onions until soft. Add garlic and cook for 1 more minute. Add tomatoes with any pan juices, chipotle peppers, cumin, oregano, salt, pepper and stock to the pan, Bring to a simmer and cook for 2 - 3 minutes.
Carefully pour the hot sauce mixture into a blender or food processor. Pulse until smooth. Pour back into the skillet, bring to a simmer and cook for 10 minutes until thickened. Add salt, pepper to taste.
Spread 1 cup of sauce in bottom of 9 x 13 baking dish.
In large bowl, mix shredded chicken, 1 cup of shredded cheese and sour cream.
Spoon about 2 tablespoon of sauce on a plate. Dredge tortilla in sauce, then flip over. Fill with 1/3 cup chicken filling mixture. roll tortilla tight and place seam side down in baking dish. Repeat with remaining tortillas and filling until all filling is used.
Spread remaining sauce over enchiladas and sprinkle with remaining 1 cup shredded cheese. Top with sliced jalapenos. Bake in 400°F oven for 10 - 12 minutes until cheese is melted and sauce bubbly.
Serve hot with lime cream, more shredded cheese and jalapeno slices.