To make the chipotle sauce, blend all ingredients together in a blender or food processor. Taste and adjust salt to personal taste. Add another chipotle pepper if you wish to make it spicier. Set aside or place in the fridge if making in advance.
To make tomato and jalapeño pico de gallo, add the tomatoes, jalapeño, onion, and garlic to a small bowl. Squeeze lime juice and add a pinch of salt. Stir and set aside or refrigerate until ready to assemble the flatbread.
When ready to cook the potatoes, heat 1/2 tablespoon of oil in a large skillet. Add sliced potatoes, making sure not to overcrowd the skillet, and cook until tender and a little crispy, about 4-5 minutes. Flip and brown the other side, cooking additional 4-5 minutes. Remove the potatoes from the skillet. Repeat as needed until all the potatoes have been cooked.
Whisk the eggs and milk together. Place butter in the skillet over medium heat. Pour in the eggs. Stirring the eggs frequently, cook the eggs until just set. Remove the eggs from skillet. And tent eggs to keep them warm. Wipe out extra egg stuck onto the skillet.
Add remaining 1/2 tablespoon of oil into the skillet. and heat over medium-low heat. Add in naan. Season with a little salt and garlic powder. Once the bottom is starting. Brown, flip over. Season with a pinch more of salt and garlic powder. Spread a generous layer of the chipotle sauce. Then layer potatoes, slightly overlapping them. Sprinkle on the cheddar cheese over the potatoes. Add the scrambled eggs. Cover and cook until brown and a little crispy on bottom and the cheddar cheese has melted. Remove from heat. Add pico and enjoy immediately!