For the chipotle in adobo, I buy a 7 ounce can, then using a blender, processor or hand blender, I puree the whole can. Use just what you need, one tablespoon in this case, then store the rest in a labeled sandwich size zipper bag in the freezer. Try to spread it out thinly in the bag so it's easy to just break some off next time you need it.
Jalapeños can be unpredictable as far as their heat. Start with a small amount in the soup and work your way to your degree of spiciness.
If you've made your own chicken broth, just use the shredded chicken from that for this soup. It's awesome!
Cotija Cheese is a hard white cheese made of cow's milk. It crumbles really well. It is not huge on flavor, but it adds a nice bit of saltiness to this. It is primarily used as a topping.