Cover guajillo peppers with boiling water. Set aside to soften while you prepare the beef. (Once softened, remove stem and seeds)
In a 6 quart Dutch oven or large heavy bottomed pot, heat oil over medium-high heat. Add beef cubes and sear until browned on all sides. Season with 1 tsp salt and 1 tsp black pepper.
Remove beef to a platter with a slotted spoon. Add onion and jalapeno peppers to the pot. Cook for 3-5 minutes until softened and beginning to brown scraping any brown bits from the bottom. Add garlic, cooking for 1 minute longer.
Meanwhile, using a blender. Blend together, stock, crushed tomatoes, guajillo peppers, reserved 1 tsp salt, chipotle, chili, cumin, cocoa, ancho, oregano, paprika, masa harina and cilantro. Cover and blend until smooth. (If you have a smaller blender, you may do need to do this in 2 batches.)
Pour sauce into Dutch oven and add beef back to pot. Stir to combine.
Cook over medium-low covered for 2 hours or until the beef is pull apart tender. Stir occasionally to prevent sticking.
To thicken, uncover and add tomato paste 1 Tbsp at a time, stirring thoroughly until melted. Repeat until desired thickness is reached. You may simmer uncovered for 15 minutes to allow the sauce to reduce further, if desired.
Serve with queso fresco, sour cream, shredded cheese, cornbread or any of your favorite chili toppings.