Heat 2 teaspoons of oil over medium to medium high heat in a large saucepan. Saute onion until starting to brown, about 5-6 minutes.
Add crushed tomatoes, oregano, basil, salt, and pepper. Simmer on low to medium low heat for 10 minutes.
During this time, heat 1 teaspoon of oil in a large saucepan over medium high heat. Saute the mushrooms and hot pepper flakes about 5 minutes. Reserve pan.
Add tomato paste to tomato sauce and mix well. Stir in vodka and mushrooms and simmer for 10 more minutes.
Start water to boil for pasta.
Add milk to sauce and incorporate well. Cook another 20-30 minutes, stirring occasionally. Keep sauce at a low simmer while cooking pasta.
Cook whole wheat pasta until al dente, about 15 minutes. Drain pasta.
Heat 1/2 tablespoon of oil in a large skillet (you can use the same pan you cooked the mushrooms in). Add pasta and stir to glaze. Add parmesan cheese and mix thoroughly. Stir in sauce. Garnish with basil, and serve.