Ok, all working properly now, I just hadnt copied the confirmation code into the SSH window properly as the error messages seemed to stop the pasting of the code correctly.
For anybody else interested in setting this up on a Raspberry Pi, in order to get the script to run automatically when booting, then use the code below as this was the only way I could get it to wait for all dependent scripts/modules/…)
Add the text below to rc.local by running a command like sudo nano /etc/rc.local and the text that should be added is (add it just before the exit 0 line).
(sleep 60
node /home/pi/assistant/index.js &> /home/pi/assistant/assistant-reboot.log) &
FYI: This will delay the start of the script until 60s after rc.local is run, which is about 30s after the Pi has finished booting (and mine is already starting quite a few other processes at boot). You will need to change directories as required.
FYI2: If you want to change the port, then it is indeed possible to change the port number in index.js. Just do a find/replace and you need to change all occurrences of 3000 to your new port (I picked 4000 as there seem to be far fewer programs that use that port). There are three occurrences that need replacing (well two need replacing, but there are three occurrences so best do all of them).