In a food processor, combine the pumpkin seeds, tahini, nutritional yeast, garlic, lemon juice, salt, and pepper. Process briefly to break up.
Add the basil and spinach and process again.
Depending on how dry the spinach and basil leaves are, you may need to add water at this stage to bring the puree together. Start with a tablespoon and puree again, adding more water as needed to reach a fairly smooth consistency.
Once the pesto reaches your desired texture, add the lemon zest and pulse.
Prepare pasta (follows), or if not using pesto immediately, refrigerate in a container (narrow and tall best to limit oxidation) for 3-4 days.
Cook the pasta according to package directions until ‘al dente’ (almost fork-tender).
Retain a small amount of the cooking water (¼ cup or so) and drain the pasta, but don’t rinse (see note).
Return the pasta to the pot and toss with your desired amount of pesto, plus a tablespoon at a time of the reserved cooking water, until the pasta is as saucy as you like.
Season to taste with additional salt and black pepper. Serve garnished with a sprinkle of crushed pumpkin seeds and basil, sliced tomatoes (if using), and lemon wedges.