Preheat oven to 350 degrees F. Scrub potatoes well to remove all dirt. Pierce with a fork, rub with kosher salt and bake on a sheet pan for 1 hour.
Meanwhile, in medium skillet over medium heat cook bacon until crisp, remove, drain on paper towels and chop. Remove all but 2 tablespoons bacon grease from the pan and heat over medium-high heat. Add onions and saute for 2 minutes. Stir in the jalapenos and saute for 2 minutes more. Add the garlic and lightly saute for 1 more minute. Set aside to cool to room temperature.
Remove potatoes from oven and let cool to a workable temperature. Slice potatoes in half, lengthwise and remove the flesh of the potato with a spoon to a bowl. Mix in butter, add pepper and salt to taste. Reserve 8 of the skin halves, discard the other 8.
Gently fold in the onion, jalapeno and garlic mixture into the potato. Combine the horseradish, sour cream, half the pepper jack cheese and the bacon; add to the potato mixture. Gently fold in the avocado.
Stuff the potatoes with mixture, top with the remaining cheese and place back in the oven on a baking sheet for 20 minutes at 350 degrees F.