Preheat oven to 350°F.
Cut the jalapeños into a boat cut. (Click the link above to see how to do a Boat Cut.)
Sprinkle insides of cut jalapeños lightly with salt and pepper, to taste.
Place the jalapeños on a cookie sheet. Place sheet in preheated oven. Cook for about 10 minutes. (Skip this step if you prefer your finished jalapeños to be more raw and crunchy.)
Remove from oven and allow to cool slightly so you can handle them.
Add cream cheese to each jalapeño to cover the bottom, leaving a concave "well" to place other ingredients. (Click the link above to see pictures of this step, if the instructions are unclear to you.) Set jalapeños aside.
In a medium pan over medium high heat, add the butter and onion. Sauté the onion until it is just starting to turn soft. It will cook further in the oven later. Remove from pan and set aside.
Place a generous slice of pastrami into each jalapeño. Press down into the boat.
Smear a good helping of the apple butter over the pastrami. The taste of the apple butter will tend to fade as it is cooked and be overwhelmed by the stronger ingredients (I couldn't taste it as all in my first attempts), so make sure you use a good amount.
Add a second slice of pastrami and another smear of apple butter.
Repeat the layers once more if your jalapeños are large enough. Heck, do it 3 or 4 more times if you like. I did three layers.
Place a spoonful of the sautéed onions on top of the last layer.
Place a couple slices of cheddar cheese on top of the onions.
Wrap bacon around each jalapeño. Secure with a toothpick, if you like.
Place jalapeños back on cookie sheet and place back in oven.
Cook, watching closely, until cheese is hot and bubbling and bacon is done, about 25 - 30 minutes. Check to make sure jalapeños and bacon are done to your liking. If not, place back in oven for more time.
Remove from oven when done and enjoy hot.