Preheat a frying pan to medium heat. After about 5 minutes, the pan should be ready to begin cooking. While the pan is heating, chop the onion into evenly-sized pieces. Bite-size pieces work well. Add a little bit of olive oil to the pan (optional), and once the pan is hot, add the chopped onion. Stir frequently. Chop 2 bell peppers into even, bite-sized pieces. Add these pieces to the pan with the onion and garlic and continue to stir frequently.
Once the water boils, add the pasta so it cooks while you are preparing the rest of the vegetables and sauce.
Prepare the spices by adding basil, marjoram, thyme, cumin, chili powder, and nutritional yeast to a bowl or plate. Add the spices and seasonings to the vegetables in the pan and stir until the spices are evenly distributed.
Finely mince 3 cloves of garlic, and add these to the pan with the rest of the vegetables and spices. Continue to stir.
Pour the diced tomatoes into the pan and stir. Cook for about 3 minutes or until the liquid is hot and bubbling.
Prepare the sauce by putting coconut milk, miso, nutritional yeast, and tapioca flour in a blender jar and mixing until smooth.
Add the sauce and stir until everything is evenly mixed together. Cook for about 3 minutes or until the sauce is bubbly and thickened.
Drain the pasta and serve topped with sauce.