I think you may have the same model as my PS4, just to confirm is it a Belize Phat?
Overlooking what you have tested to resolve the issue it maybe a internal hdd issue, if you are using the exact same files (minus the initramfs because Nazkys is specifically for internal) and USB starts the installation without errors then it must be either a issue with the internal hdd OR one of the files you are using is incompatible with your ps4.
-Have you tried deleting/re initializing your internal hdd from the recovery menu on the PS4? keep in mind this will delete all current data stored on hdd but will not affect the firmware.
-Are you certain you are using the correct initframs for internal hdd installation?