I have an iPhone 5s that needed the motherboard replaced and I don't have the original touch id for it. Is there anyway to program the button. I can jb it if needed.
You're going to need to take it into an Apple store most likely so they can do it for you. If there isn't one near you, you can probably mail it in to Apple so they can perform the needed service on the TouchID.
Try taking it into a store without mentioning you changed the motherboard yourself. They might do it, but will almost certainly charge you for it since it is out of warranty.