somehow it seems drivers got twerked. Uninstall current usb drivers for the device and try reinstalling them after you reset your phone and the computer. (device shouldnt be plugged in when installing.)
If you can get the usb drivers to work , id suggest using ODIN to flash back to stock. Here's a link to a guide for that ---> How to Unroot Galaxy S4 and Remove Root Completely! | GalaxyS4Root.com
you can download the stock firmware here:
--> Galaxy S4 Stock Firmware | GalaxyS4Root.com
If you really want custom stuff on there after that , you can just re-root etc and start over fresh. Good luck!