Amy, i know this doesn't answer your problem, but for info sake, i do remember hearing and actually seeing for myself, that when the s4 first came out people's phones were only charging to 99% and then a few minutes off the charger they would drop down to 17%. At least that's what the phone was displaying. I had heard that was fixed in an update tho.
So i guess my question would be, have u taken an update since u rooted your phone? I may be way off base, but if ur looking for any answer to help b4 u decide to repair it, u might want to look into that