I think most of your problems stem from the fact that your /storage partition is low on memory (the library is stored there) you can check that by going to Setup -> System Info -> Storage and looking at /dev/mmcblkp3.
Available should be something like 2G.
The reason that we cannot put this on the hard drive is because the HDD is formatted as exFAT and the linux kernel cannot access an exFAT partition at boot time to access the setup files it needs.
It is possible to move the /storage to the hard drive, but this requires that the HDD is first reformatted as an ext4 file system (which will then wipe any media currently stored on the HDD).
Basically to do this you'd need to re-partition the HDD into two partitions, a 900G exFAT partition and a 100G ext4 storage partition.
Let me think about how I can do this, really simply