Ok, I think I’ve figured this out, and have a solution.
Our script is blindly grabbing the 2nd line of the df -k output to check for disk space. This works on a default Pi with no additional drives, but falls on its face here. Needs improvment! 
To fix it, let’s make the script check /dev/sda1 instead:
In the folder where you found setup.sh, run
sudo nano setup.sh
to edit it. Locate the line which you showed me:
availableSize=df -k | head -2 | tail -1 | awk '{print $4}'
and change the 2 to a 4. This will make it read the 4th (and correct) line of your df output. Save your changes.
Next, to run the script that we edited, we need your Pi invite code. You can find this as the part after the underscore on your downloaded install script. So if you have file rpi_q6k588d6wb.sh then your invite code is q6k588d6wb
Finally, browse back to the folder that contained setup.sh that we edited. Run it again with the following command: sudo ./setup.sh -code YOURINVITECODE -v where you replace YOURINVITECODE with your actual invite code.
That should kick off the rest of the install which should work automatically. Apologies for the trouble, we need to update this install script to be more robust for multiple drive cases like yours!