In a large bowl, mix flour, pepper, and thyme, then lightly coat the meat with the flour mixture.
Heat 2 Tbsp oil in a large stock pot and brown meat in two batches. Remove beef from pot.
Add 2 additional Tbsp oil and onions to the pot and cook until the onion is translucent. Stir in reserved flour and brown 2-3 minutes.
Add coffee stock, tomato paste, Worcestershire seasoning, and molasses to mixture and stir well.
Add the meat chunks.
Bring to a boil then reduce heat and simmer 1 - 1½ hours. (2 hours or more in a crock pot)
Add potatoes, mushrooms, and carrots, and return to simmer for an additional 30-45 minutes or until vegetables are tender. Add peas and cook covered 8-10 minutes until peas are crisp-tender.