Preheat the oven to 350 degrees F. Heat a large skillet over medium high heat. Saute the onion and garlic with 1 tablespoon butter for 2-4 minutes. Add the shredded meat, masa, tomato paste, cumin, thyme, and chopped chipotle peppers. Stir well and add 1 cup of water. Bring to a boil and lower the heat to simmer. Simmer until all the liquid in rendered out--approximately 10 minutes.
Meanwhile, mix 2 cups of masa with the baking powder, salt, and cumin. Add the beef stock and mix to a crumbly consistency. Pour in the melted shortening and mix by hand until smooth.
Spray mini muffin tins with nonstick cooking spray. Scoop the masa mixture into small 2 teaspoon balls using a small cookie scoop and place in the muffin tins. Use a round teaspoon (or pestel) to press a deep indention in the center of the masa balls. Once the beef mixture has rendered out the liquid, stir in the sour cream and lime juice. Salt and pepper to taste.
Fill each masa shell with the meat mixture. Bake for 20 minutes. Allow the tamale bites to cool 5-10 minutes before extracting them from the muffin tins. Use a small sharp knife to loosen the tamale bites from the muffin tin. Then lift one side with the tip of the knife and gently lift each tamale bite out with your fingers. Garnish with crumbled queso fresco and thyme leaves. Serve warm.
Tamale Bites can be served warm or at room temperature. They can also be rewarmed once they are out of the muffin pans.