Preheat oven to 375°F. Line bottom and sides of a jelly roll pan with parchment paper. Grease paper and set aside. In a small mixing bowl, beat cream cheese and milk with an electric hand mixer until smooth. Add flour and salt, mix until combined. In a large bowl, beat eggs until well-mixed. Add cream cheese mixture. Set aside.
In a large skillet, sauté peppers and onion in oil until translucent, approximately 8-10 minutes. Combine vegetables with the egg mixture. Spread on the prepared jelly roll pan. Bake for 30-35 minutes, or until eggs are puffed and set. Remove from oven.
Immediately spread with mustard and sprinkle with 1 cup of the cheese. Top with ham and finish with an additional cup of cheese. Roll up from short side, peeling the parchment paper away while rolling. Sprinkle top with the remaining cheese. Bake an additional 3-4 minutes or until cheese is melted. Cut into 1 – 1 ½ inch thick rolls, sprinkle tomato on top.