Preheat oven to 375 degrees. Bring a kettle of water to boil and cook rotini to al dentè. Drain and set aside.
Heat olive oil in a large sauce pan over medium heat.
Add 1 tablespoon minced garlic, green pepper, and onion. Sauté for 4-5 minutes, until just tender.
Add salt, red pepper flakes, basil, oregano, zucchini, and mushrooms. Cook for an additional 5 minutes.
Stir in diced tomatoes and tomato sauce, allowing to simmer while you mix the cheese mixture.
In a separate bowl, mix ricotta, 1 cup of the mozzarella, 1/2 cup of shredded parmesan, egg, 1 teaspoon of minced garlic and pepper.
Layer approximately 2 cups of the vegetable mixture on the bottom of a pyrex pan.
Add approximately 1/3 of the noodles and then 1/3 of the cheese mixture.
Continue layering until two more times, but end with the vegetable mixture.
Sprinkle with remaining mozzarella and parmesan. Add a little basil and oregano if you're feeling fancy.
Bake for 30 minutes, or until the cheese is melted and the mixture is heated through. If you loved browned cheese, urn on the broiler at 500 degrees and cook for 1-3 minutes more, watching VERY closely.