This is a recipe for the spice paste itself, which you then use, often diluted, in a variety of recipes from the Maya region of Central America, from the Yucatan to Honduras.
Preheat your oven to 425°F. Remove the stems from the dried chiles and arrange them in a large roasting pan, ideally in one layer. Roast them until they are completely black and smoking (use your oven fan!!!), about 15 minutes or so. Turn off the oven but leave the chiles in there another 30 minutes.
While this is happening, it's a good idea to take out your tortillas and set them on the counter. You want to work with stale tortillas the following day.
Move the chiles to a large pot and just barely cover with water. Crush and mash them with a potato masher or somesuch. Don't puree them. Put all the chiles into a strainer that you have lined with cheesecloth. Squeeze out all the water. Discard this water, which will taste like an ashtray.
Put the chiles back in the pot, or a bowl, and cover with water again. Use running water to clean your cheesecloth into the bowl, so you catch the bits of chile stuck to it. You will want to soak the blackened chiles overnight, changing the water 2 times. Just pour off the water each time, no need to use the cheesecloth for this.
The next day, char your tortillas. If you have a gas burner, this is easy: Set them on the burner until they catch fire, blow them out, and flip and char the other side. If you just have electric, you can do the same thing but it's not as easy. You can also just set them on a very hot cast iron pan or griddle until you get lots of blackening.
Crush the tortillas and put them in a blender. Add to the blender the achiote paste and the achiote verde, if using.
Toast the peppercorns, allspice berries, cumin seed and cloves in a dry pan until everything smells wonderful. Grind this in a spice grinder, then add to the blender.
After you've charred the tortillas, you will need to char your onion and garlic. Separate the cloves of the garlic without peeling, then blacken the skins on a comal, griddle or cast iron pan. Do the same with the quartered onion, charring the two cut sides of the onion quarters. Chop all this an add to the blender.
Strain the chiles, reserving the water. Add that, the chipotles and the Mexican oregano to the blender. Puree all of this thoroughly, adding the soaking water as needed to make the blades run smoothly.
Now, set up that strainer and cheesecloth again and pour the contents of the blender into it. Squeeze out as much water as you can.
Finally, scrape the mixture into a clean bowl and add the vinegar and salt. Mix well, pack into glass jars, and store in the fridge. It will last, more or less, forever.
Notes
Keep in mind that my chile suggestions are not authentic, but realistic. In a perfect world you'd use a thin walled, medium spicy pepper. Chile puya is a perfect choice, but isn't always available in markets. Pasilla apaseo, salsero or chiles de pais are all excellent choices.
Keys to Success
This is an involved recipe, but it will last a long time in the fridge, so you need only make it once in a while to have a good supply.
The achiote paste is in pretty much every Latin market in America, so that shouldn't be a stopper for you. Ditto for Mexican oregano. Both are available online, too.
Do not skip the water changes in that first overnight soak. It's vital to the success of the recipe, taming the bitter, acrid taste of the freshly burnt chiles.