Preheat oven to 400 degrees F. Coat a 9"x 13" baking dish with cooking spray.Cut zucchinis in half lengthwise. Scoop out pulp and seeds, leaving 1/4-inch shell (use a small spoon for this). Reserve pulp from both zucchinis and chop.
In a medium bowl,combine pulp,garlic,tomato, mushrooms,basil,oregano,crushed red pepper flakes,olive oil and 1/2 cup cheese. Divide mixture evenly between zucchini shells. Place stuffed zucchinis in prepared baking dish.
Cover with foil. Bake 25 minutes,or until zucchinis are tender. Sprinkle with remaining cheese. Bake uncovered 5 minutes more or until cheese is melted. Top with fresh basil and serve.