[Can] I restore only /system and boot my original ROM ?
It depends upon what lies in the backup. If you took the backup of your stock ROM and you're referring to the same backup, then yes, restoring /system using that particular backup would restore stock ROM. But you would need to restore /boot as well since that is part of stock ROM too.
However, if you must restore a different ROM, even if it is a stock ROM, it is a good practice to do a clean flash or atleast overwrite existing /data and /cache files with the ones in the backup to avoid conflict between various versions of files/apps which can cause bootloop or battery drain or whatnot.
In your case, since you cannot restore /data from the backup, I advise you to take a complete backup of your current ROM (including userdata), then reset /data (except /data/media) and /cache, and then restore /system and /boot from stock ROM backup. In this way, you would end up with a pristine stock ROM and can always restore /data when you manage to fix that error you mentioned. This is the path of least problems.