Melt the butter in a skillet over medium heat, cook until the milk solids turn amber, and stir in the sage for 30 seconds.
Boil the shells in water with 1 teaspoon salt for 3 minutes less than the package directs and drain.
Place the pasta, brown sage butter, evaporated milk, whole milk, squash, mustard, pepper and remaining salt in a 6-quart crockpot.
Cook on low for 45 minutes, then stir in the cheddar and fontina by handfuls.
Cook on low for 45 to 60 minutes more until the pasta is tender and the orange sauce is smooth.