For the bread pudding cups: Preheat the oven to 350 degrees F. Prepare a muffin tin with paper liners and spray the liners with nonstick cooking spray. (Alternatively, spray the insides of twelve 2-ounce ramekins with nonstick spray.)
In a large bowl, whisk together the half-and-half, brown sugar, cinnamon, vanilla, salt and eggs. Add in the pecans, butter and bread and stir to coat. Let the mixture sit for 10 minutes.
Carefully fill the muffin tins about two-thirds of the way up with the bread pudding mixture. Cook until the puddings set, about 25 minutes.
For the bourbon sauce: In the meantime, add the cider, bourbon, brown sugar, butter, lemon juice and salt to a saucepan over medium heat and bring to a simmer. Simmer until the sauce reduces by one-half, about 10 minutes.
Remove the bread puddings from the oven and let cool for 10 minutes. While still warm, use a skewer to poke a few holes into each pudding and pour in a couple of tablespoons of sauce. Serve immediately.