Brown the sausage in a skillet for 9 minutes, crumbling it until it reaches 160°F, then drain it thoroughly.
Boil the shells in water with 1 teaspoon salt for 3 minutes less than the package directs and drain.
Butter a 6-quart crockpot and add the pasta, sausage, roasted peppers, evaporated milk, whole milk, pepper and remaining salt.
Cook on low for 45 minutes, then stir in the fontina and provolone by handfuls.
Cook for 45 to 60 minutes more until the pasta is tender and the sauce clings to the shells.