E04- Not necessarily an issue with the Array, but more an issue with booting up. When the unit is booted into EM mode, it will not find the array (this is normal). Most likely if the unit lost complete power to it while it was running, there is a firmware issue (either the firmware itself or the flash chip or the boot partition on the drives).
Does the firmware update ever finish with a message saying it completed?
The unit should reboot three times during the update, do you know if it does all three?
When you do run the firmware update, have you tried forcing the unit into EM mode by holding the reset button as you boot it up or just let boot into EM mode on its own?
What operating system is on your computer?