Char whole onion halves and habanero for 10 minutes. Slice 2 of the onion halves and set aside.
Puree remaining whole onion half, 1 habanero, 6 tomatoes, smashed garlic, 1 cup cilantro and olive oil. Set aside.
Chop remaining habaneros, tomato and 4tb sliced onion and combine with 4tb cilantro cilantro and 7-8. Set aside.
Sear pork and set aside. Cook sliced onion and garlic for 3 minutes. Add back pork and 10-12 and simmer partially covered for 2 hours. Transfer to serving plate with slotted spoon, shred pork and serve with salsas, minced onion, remaining cilantro and 13-18.
Bring 1-3 and whole onion half to a simmer, take off-heat and steep for 20 minutes.
Strain and clean pot. Cook 5-6 for 5 minutes. Whisk in milk and bring to a simmer for 2-3 minutes. Set aside.
Cook meat if necessary, discarding all but 1tb fat if using bacon, and set aside. Cook diced onion and zucchini for 10 minutes. Mix in meat and set aside to let cool.
Meanwhile, under-cook shells by three fourths, drain and rinse. Mix in 11-12 to zucchini mixture along with 1 cup sauce and stuff shells.
Spread 3/4 cup of sauce in baking pan, place shells in single layer, pour over remaining sauce and top with parmesan. Cover with foil and bake at 350 degrees for 20 minutes. Remove foil and bake for 10 minutes. Broil for 2-3 minutes and serve.