Preheat oven to 400 degrees F and grease a 2 quart casserole dish (9x13 inch pan works too).
Boil pasta according to package until al dente.
Meanwhile, in a medium sauce pan, melt butter over medium high heat. Whisk in the flour until lumps are gone. Whisk in 1/2 cup of milk until smooth and then slowly stir in the remaining milk and add the salt (taste and add more salt if desired) and pepper. Simmer for 6-8 minutes while continuing to stir (you must stir or else it will curdle) until thick. Remove from heat and stir in all but 1/2 cup of cheese.
Fold cheese mixture into cooked and drained pasta and then place in casserole dish. Top with remaining 1/2 cup cheese, sprinkle with fresh cracked pepper, and bake for 15 minutes or until golden and bubbly. Let it rest 5 minutes before serving.