For the Pork Marinade: Toss unpeeled garlic in a dry skillet over high heat until starting to toast and get dark spots. Peel the skins when cool enough to handle.
Heat oil in a skillet over medium heat until shimmering. Add achiote, oregano, cloves, cinnamon, black peppercorns, cumin, and allspice and cook, tossing and stirring, until fragrant, about 2 minutes.
Transfer this mixture to a food processor along with garlic, orange juice, lime juice, vinegar, soy sauce, and kosher salt.
Blend until smooth. Season to taste with more salt if needed.
Place pork in a roaster pan. Pour marinade over meat and rub it in with your hands. Cover, refrigerate, and let it rest at least 3 hours and up to overnight.
To Cook The Pork: Preheat oven to 300 degrees.
Drain tomatoes. Slice peppers and onions and tuck them along with bay leaves within the layers of the pork.
Cover with foil and cook 3 hours.
For the Enchilada Sauce: In the meantime make homemade enchilada sauce (recommended) Or open cans of purchased enchilada sauce to equal 4 cups. Place in a wide bowl and set aside.
Shred pork with two forks, soaking it in drippings.
To build the enchiladas: I like to use 2 - 3 10 1/2" by 7" casserole dishes. They're a perfect fit for corn tortillas.
Pour just enough of the enchilada sauce to cover the bottom of the casserole dishes by about 1/2 inch.
Set up your assembly line in this order. Skillet to fry tortillas, plate to place the tortillas once they're fried. A bowl of enchilada sauce (bowl should be wide enough to easily dip fried tortillas, a bowl of shredded pork, the shredded cheese and a casserole pan lined with enchilada sauce. Keep a couple of sets of tongs handy to handle food.
Heat 1 tablespoon of the oil in a heavy skillet over medium high heat. Once the oil is hot, fry the corn tortillas. Using tongs, place a single corn tortilla into the oil and cook or 30 seconds. Turn the tortilla over and cook for an additional 15 seconds. Remove the tortilla to a plate and cover with a paper towel to keep warm. Repeat with the remaining tortillas, adding more oil when necessary and stacking the tortillas on top of each other and keeping the paper towel on top. Expert tip: the corn tortillas will break if the oil is not hot enough. Keep that heat at medium high. The tortillas should be soft, not crispy. You want to be able to roll them easily.
Place 2 cups of the enchilada sauce into a shallow bowl. A deep dish pie plate works very well. Using tongs or your hands, dip a warm tortilla into the enchilada sauce and then place the tortilla into one of the casserole pans.
Add a spoon full of the shredded pork, then a pinch of shredded cheese. Don't over-fill the tortillas or they'll break. Roll the tortillas and place them seam side down in the pan, moving the tortilla to the end of the casserole so you can add more rolled tortillas. Repeat.
Once the enchiladas are rolled, sprinkle liberally with more grated cheese and spoon more enchilada sauce over the top. About 3/4 of a cup of sauce will do.
Bake the enchiladas until bubbly. 350 degrees for 20 - 30 minutes.