Combine ham or sausage, onions, and 1 C cheese in a medium bowl. Spoon a scant 1/4 C down the center of each tortilla. Roll up and line up, seam side down (two along the edge) in a greased, 15 x 9 x 2 glass baking dish.
In a large bowl, beat milk, eggs, salt and flour until smooth.
Pour over tortillas. Cover with foil and refrigerate for 8 hours, or overnight. Remove from refrigerator 30 minutes before baking.
Bake covered, at 350°F for 30 minutes, uncovered for 10 minutes. Sprinkle with remaining 1 C cheese and return, uncovered to oven until cheese melts-about 4 minutes.
Let stand 10 minutes before serving.
Garnish with a dollop of sour cream and a 1/4 cup of salsa.