Cut zucchini in half lengthwise; scoop out pulp and seeds, leaving 1/4-inch shell (use a small spoon for this). Reserve pulp from two zucchini and chop. Combine zucchini pulp, garlic, tomato, mushrooms, basil, oregano, crushed red pepper flakes, olive oil and 1/2 cup cheese in a medium bowl. Divide mixture among zucchini shells.
Place stuffed zucchini in a 13 x 9 baking dish; cover with foil. Bake for 25 minutes or until zucchini is tender. Sprinkle with remaining cheese. Bake uncovered 5 minutes more or until cheese is melted. Top with fresh basil.