except for data & shares everything else need to be reconfigured, name, IP, users, passwords, remote access etc after the system only restore.
backups are always important and especially before any major operation. WD says the system only restore leaves data and shares in place, I have done it once with no issues and i have not seen anyone else report issues with it either
DO NOT do either of the factory restores as they delete all data
Except for the hassel of re-configuring it should not be an issue to do the system only restore
one other point when creating the users and setting the user share permissions take your time do one at a time. I believe rushing this is what has caused the overall_share issues