In a medium bowl, combine whole-wheat flour, all-purpose flour, brown sugar, thyme, baking powder, and salt.
In a separate bowl, whisk together milk, egg, melted butter, and butter extract until well combined. Add milk mixture to flour mixture, whisking until smooth. Spoon about 1/4 cup mixture into each compartment of a waffle iron. Close cover, and cook for 2 to 4 minutes, or until done. Using a 3 1/2-inch round cutter, cut waffles into rounds.
Place 1 waffle round on top of each Shirred Egg in muffin pan. Place cutting board on top of pan. Carefully invert pan. Top each portion with a cooked round of pancetta. Serve with Lemon-Thyme Butter Sauce. Garnish with fresh thyme and cherry tomatoes, if desired.