There is no "real" recipe to Jon's chili beyond the base set of ingredients and improvisation with spices and available ingredients. If there are fresh peppers, they go in. If there's homemade salsa, it definitely goes in. Beer (Shiner Bock I find is best) cuts the spice level nicely without removing the flavor.
I sautee the onion/garlic/jalapenos until tender, then add the meat and brown it. Add the tomatoes and cook for 5 minutes, then add whole habaneros and the first spices (salt, pepper, first group of spices). Add 4 cups of water and some beer and bring to a boil.