Remove the USB from your computer and plug in to the PS4 MD5 CHECK ANY PUP FILES BEFORE INSTALLATION! - HERE Make a folder on the root of your USB stick called, inside that a folder called, and put the for your chosen firmware in there (PUP's are found below).
On PC: Format your stick to EXFAT using any suitable formatting tool.
If this doesn't work a full factory format will be required to remove the pending update nag.