If I remember correctly, all the USB disk for the 3400 series has is the settings and paramaters of the device at the time you make the USB stick. It doesn't actually boot the device itself.
The 3400 series will boot into emergency mode, no USB is needed for the boot process.
I would wipe the drives again with diskpart.
With a clean set of drives, you should be able to run the firmware updater again from a windows PC in the debug mode. Use the debug mode with all options checked for update (left side) and config (right side) to format and rebuild.