Macaroni and Cheese w/Onions & Bacon

(from Williams Sonoma New American Cooking)
4 thick slices bacon
3 Tablespoons butter
1 small sweet onion
1-½ cups fresh bread crumbs
1-½ teaspoons chopped fresh thyme
¾ teaspoons salt
¾ teaspoons pepper
1 pound elbow macaroni
2 Tablespoons all-purpose flour
2 cups low-fat or skim milk
4 cups shredded, sharp cheddar cheese
Preheat oven to 350 degrees. Grease a 1-½ quart baking dish with butter.
In a frying pan over medium heat, fry bacon until crisp, 6-8 minutes. Transfer to paper towels to drain, then chop coarsely. Discard all but 1 Tablespoon of drippings from the pan.
Return pan to medium-high heat, add 1 Tablespoon butter. When it melts stir in the onion and cook stirring often, until golden, 3-4 minutes. Stir in bread crumbs, bacon, thyme, and ¼ teaspoon each salt & pepper. Remove from heat.
Meanwhile, bring a large saucepan ¾ full of water to a boil. Add salt to taste and the macaroni. Stir well and cook 8-10 minutes. Drain well & pour into baking dish.
In a small saucepan over medium heat, melt the remaining 2 Tablespoon butter. When it melts, whisk in the flour and continue to whisk for 1 minute. Gradually whisk in the milk until smooth. Simmer, stirring occasionally, until lightly thicken, 2-3 minutes. Whisk in the cheese until melted and smooth. Add the remaining ½ teaspoon each of salt & pepper. Pour over macaroni. Sprinkle with bread crumb mixture.
Bake 35-40 minutes until brown and bubbling.