Place the beef chunks and marrow bones in a large bowl, pour the fresh lime juice over the meat, toss to coat, and let rest for 15 minutes. Rinse thoroughly under cold water, drain well, and season generously with salt and black pepper.
Add the onion, garlic, scallions, parsley, thyme, and green bell pepper to a blender and blend into a smooth, bright green paste, adding a splash of water only if needed. Spoon about half the epis over the seasoned beef, rub it in well, and let marinate for at least 30 minutes or up to overnight.
Heat the vegetable oil in a large stockpot or Dutch oven over medium-high heat. Add the marinated beef and marrow bones and sear on all sides until deeply browned, about 8 minutes. Stir in the tomato paste and whole cloves and cook for 1 minute until fragrant.
Pour in the beef broth, add the whole scotch bonnet pepper, cover, and simmer over low heat for 1 hour and 30 minutes, until the beef is fork-tender.
While the beef simmers, place the cubed calabaza or kabocha squash in a separate pot, cover with water, and boil for 20 to 25 minutes until completely soft. Drain and blend with a ladle of its cooking liquid until perfectly smooth; set aside.
Once the beef is tender, remove and discard the whole scotch bonnet pepper. Stir the squash puree into the pot, then add the carrots, potatoes, turnip, malanga, and celery. Stir in the remaining epis paste and simmer uncovered for 20 minutes, until the vegetables begin to soften.
Add the chopped cabbage to the pot and stir to combine. Break the vermicelli or spaghetti into short 1-inch pieces and add to the soup. Simmer for another 10 to 12 minutes, stirring occasionally, until the pasta and remaining vegetables are fully cooked.
Taste the broth and adjust the seasoning with more salt and black pepper as needed. Ladle the hot soup into bowls, making sure each one gets a good mix of beef, vegetables, and pasta, and serve immediately.