Bring a large pot of water to a boil. Add the macaroni and cook according to the directions on the package, 6-8 minutes. Drain well.
Meanwhile, heat the milk in a small saucepan, but don't boil it (I sometimes just microwave). Melt 6 tablespoons of butter in a large (4 qt.) pot and add the flour. Cook over low heat for 2 minutes, stirring with a whisk. While whisking, add the hot milk a little at a time and cook for a minutes or two more, until thickened and smooth. Off the heat, add the pepper jack, cheddar, salt, and pepper. Add the cooked macaroni and stir well. Pour into a 3 quart baking dish.
Slice the tomato and arrange on top with the jalapenos. Melt the remaining 2 tablespoons of butter, combine butter with bread crumbs, and sprinkle on top. Bake 30-35 minutes, or until the sauce is bubbly and macaroni is browned on the top. If you want it more browned, try broiling ti for 2 minutes at the end.