In a medium skillet, sauté red pepper, green pepper, and 1/2 cup onion in 1/4 cup butter until crisp-tender.
Add oregano, garlic powder, cayenne pepper, salt and pepper, flour, and heavy cream; stir well. Continue cooking for about 3 minutes or until slightly thickened. Add 1-1/2 cups Pepper Jack cheese; stir until melted. Add sour cream, stir to blend. Set aside.
In a large skillet, melt 2 tablespoons butter. Sauté shrimp and 1/2 cup onion until shrimp are pink. Remove shrimp to a cutting board and chop; return to butter and onion. Add chopped tomatoes and 1/2 of the cheese sauce.
Spoon about 1/3 cup shrimp mixture into each tortilla. Sprinkle Pepper Jack cheese on top of shrimp mixture. Roll up tightly. Arrange seam side down in a 9x13-inch glass baking dish, sprayed with non stick cooking spray.
Spoon remaining cheese sauce over tortillas and sprinkle with remaining Pepper Jack cheese. Bake at 350 degrees for 30 to 35 minutes. Garnish with fresh chopped cilantro.