Rinse off the Morita chiles and pat dry. Lay them on a parchment-lined baking sheet, aand roast in a 400 degree oven for 8-10 minutes. Once done, put them in a bowl and cover with hot (almost boiling) water. Top with a plate to weigh them down, and allow them to sit for 30-35 minutes.
Place the tomato on the parchment lined baking sheet and roast for 7-10 minutes. Remove and set aside.
Drain the chiles from the water and set 1/2 C of the water aside. Slice the top (stem) off of the chile, and then down the side. Remove the seeds and discard. Place half of the chiles in the blender with 1 whole onion, tomato, 2 cloves garlic, brown sugar and 1/2 C. water (feel free to use the soaking water if it isn't too bitter). Puree until smooth..
In a skillet, add your oil, the other diced onion, remaining garlic and spices and saute until soft. Add the chipotle puree from your blender, remaining chipotles, additional 1/4 C. water, and apple cider vinegar. Simmer for 20-25 minutes until the sauce reaches your desired consistency.
Add additional salt, pepper or spices as needed. Store between 2 pint size jars or three 8 oz jars.