Just to check, when you plugged the iPhone in and it didn't charge, was the ignition on or off, if on was the engine running or not?
I don't know your knowledge on electrics or the electrical set up of the Z1000sx.
So just in case
The USB is on a switched live feed, if the ignition was off then that's your issue, there was no power to the USB itself.
If the ignition was on and the iphon didn't charge have you got another device you can plug into the USB to see if that gets power?
I've have a dual output with lcd volt display USB and never had any issues with charing phones etc etc using it (with ignition on)
If you are swapping the USB units over you can do it without taking the fairing off and just un doing the black trim that the USB is housed in, a little fiddly but doable.