add all ingreadents except pasta and cheeses into a large sauce pan bring to a boil stirring to make sure bottom does not burn,turn to low heat cover with lid and simmer 30-120 minutes stirring ocassionally so not to burn.(the longer you cook the sauce the more pepperoni flavor you will have I cook it for at least 2 hours).
While the sauce is simmering cook your pasta according to the directions on package.
Heat oven to 350.
mix sauce with pasta.
Grease a 13x9 inch pan.
Layer half the pasta ingredients in pan add a layer of each of the cheeses.
Repeat then top with rest of cheeses.
Bake, uncovered for 25-30 minutes, until light brown.