Preheat oven to 350 degrees. Line a 12-count muffin tin with paper liners and set aside.
In a large pot of salted, boiling water, cook shells just shy of al dente (about 6 to 7 minutes).
Meanwhile, melt butter in a skillet over medium heat. Stir in flour to form a roux and cook for about one minute.
Slowly whisk in milk until incorporated. Bring mixture to a boil then reduce heat and simmer until thickened (about five minutes), stirring occasionally. Remove from heat.
Stir in mustard and season with sea salt and black pepper to taste. Stir in parmesan cheese and 2 cups of cheddar cheese until sauce is smooth then fold in the cooked shells.
Fill prepared muffin tin with mac & cheese mixture and sprinkle half of remaining cheese over the top of each muffin. Bake for 20 minutes or until tops are golden and bubbly.
Let muffins sit in pan for 10-15 minutes in order to cool slightly before handling. Otherwise, they will fall apart.
Repeat baking process with remaining mac & cheese mixture. Should make 24 muffins in total.
Notes
Store refrigerated in an airtight container and reheat individual portions with a splash of milk or cream.
If you want your mac & cheese to stay as moist as possible, reheat it in the oven rather than the microwave. Per the above, I'm a microwave gal myself.
To retain moisture, cover the mac & cheese before reheating. Either loosely with a microwave-safe top in the microwave or with foil in the oven.
With either method, add a splash of milk or cream to your mac and cheese portion (one tablespoon per cup of pasta) before reheating.
It's best to reheat only the mac & cheese about to be eaten because the more times macaroni and cheese is reheated, the dryer it gets. So these baked mac & cheese muffins are actually ideal for reheating.
I recommend sprinkling a bit more shredded cheese on top once it's all done but that's up to you.