Core tops of tomatoes and cut an "x" in the bottom of the skin. Place in boiling water for 2-3 minutes - immediately remove and place in an ice bath. Allow tomatoes to cool and (easily) take off skins.
Puree tomatoes in a blender to the desired consistency. Pour into a large stock pot. Add tomato paste, lime juice, and spices.
Roughly chop the remaining vegetables, reserving ½ of the red onion and ½ bunch cilantro for the end. Adjust jalapeño amount as needed for spice level. Place ingredients in the blender and puree. Add to tomato mixture to stock pot.
Put the large pot over medium heat and bring to a boil. Reduce heat to low and simmer for 3-4 hours, until salsa has reduced by about ⅓. Stir occasionally.
Cool to room temperature. Puree reserved red onion and cilantro in your blender and mix into salsa. Pour into quart-sized freezer bags (this recipe made roughly 8 cups of salsa for me). Freeze for up to 6 months or store in the fridge for up to a week.