I would try to restore via sd card as explained here:
https://wiki.mobileread.com/wiki/PRST...bricked_device
then flash latest sony firmware
then re-root.
finally: don't mess with system files next time unless you know what you're doing
regarding usb connection - it should be still thereafter rooting - just tap on the notification area (top bar of the screen) and then tap on "connect via usb"...