In the oven, place one rack in the lower third and the other in the upper third position. Preheat to 375°F.
Whisk the eggs together with the milk, salt, pepper, and chives in a large mixing bowl. Grease a 9x13 baking dish with cooking spray, and pour the egg mixture inside. Place on the lower rack of the oven. Bake until the eggs are puffed around the edges and a knife inserted in the middle comes out clean, 25 to 30 minutes. Cool completely.
Meanwhile, make the bacon. Line a baking sheet with foil. Lay the bacon down in a single layer with no pieces overlapping. Turn up the edges of the foil to catch any grease. Place pan on the upper rack of the oven and bake for 15 to 20 minutes. When finished, transfer the bacon to a plate lined with paper towels to drain. When cool, break each piece in half to make them easier to fit on the sandwiches.
When the eggs and the bacon are both finished, place the English muffins cut-side-up on a baking sheet and toast in the oven for just a few minutes until the edges are crispy.
Use a spatula to lift the eggs out of the pan and onto a cutting board. Using a large biscuit cutter or drinking glass, cut 6 rounds out of the eggs. Use the scraps for new sandwiches, or other dishes.
To assemble the sandwiches lay the bottom halves of the English muffins in a row on a cutting board. Top each one with an egg round, a slice of cheese, and 2 pieces of bacon. Finish by adding the muffin tops.
If you are consuming right away, heat the sandwich in the preheated oven for 2-3 minutes until the cheese melts.
If you are freezing the sandwiches, wrap each one in aluminum foil. Put all the sandwiches in a freezer bag for storing. Freeze for up to 1 month.
To Reheat: Uunwrap the frozen sandwich and place it on a microwave-safe plate lined with a paper towel. Heat at full power for 1 to 1 ½ minutes, or until the cheese is melted and the egg is warmed throughout. Toast muffin separately if you want a crunchier sandwich.