by Ken Task.
You've got one thing in your favor ... running linux! ;)
Qualifications for this response ... help admin a server that has had 'larger' courses ... from 20+ Gig up to and including (believe it or not) a 139Gig course ... (don't ask!!!!).
Using the command line backup.php script in moodlecode/admin/cli/ was successful in backing up those large courses ... one at a time. Note the backup script takes preferences from Moodle Admin UI setup of what to backup as it's defaults and no way to change those via command line (I'd remove stats and logs in preferences for backups for a big course backup run - then turn them back on later).
The 'trick' ... is to use 'nohup' in front of the php command to run the backup.php script.
Since I see Ubutnu in your output of moosh, here's a reference:
http://manpages.ubuntu.com/manpages/trusty/man1/nohup.1.html
from moodlecode/admin/cli/ looks like:
nohup php ./backup.php --courseid=INTEGER --destination=STRING
The destination was to a partition that had enough space for the approximate size moosh info would provide ... so --destination=/mnt/data/moodlebackups/ was my destination.
For that 139Gig course to backup had to shutdown apache service to gain enough memory so that php and mySQL were the only apps involved - and with nohup it ran almost all night long.
I use CentOS or RHEL and have used nohup on those flavors. Works.
I don't see anything in the error related to questionbank, but do see mention of a theme.
Is that theme installed/compat with the version of Moodle to which the large backup is being restored via Moosh?
Since you mentioned your process ... the course backed up then restored to begin a new fresh course with same content ... are your resetting the course first ... selecting options to remove all student and student work from the course leaving only the teacher?
'spirit of sharing', Ken