In the same large sauce pan that you used to cook the chick'n and mushrooms in, add vegan butter on medium heat. Once the butter has melted, add shallot and chopped
stems to the pan. Sprinkle with salt, pepper, and thyme. Cook, stirring often, until the shallots are translucent, 5-7 minutes. Add garlic, and cook another 2 minutes. Sprinkle the flour over the shallot, ad stir to incorporate.
Reduce heat to medium-low, and slowly add in the marsala wine. Stir to incorporate. Slowly add in prepared broth. Bring to a simmer, and continue to cook until it's reduced by about 1/3, about 20 minutes.
While the sauce is simmering, start stuffing your shells.
Using about one tablespoon of the filling, stuff each shell gently. Repeat until all the filling is gone; you may have a few shells left over.
Spread 1/3 of the Marsala Cream Sauce in the bottom of a 9"x13" baking pan. Place Shells over the sauce in a single, even layer. Sprinkle mozzarella shreds evenly over the shells, then cover with remaining sauce. Place in preheated oven and bake until golden brown and bubbly, about 25-35 minutes. Remove from oven and let cool about 5 minutes. Garnish with parsley and enjoy hot.