So, I have been looking around and found these two threads. I think they are very relevant to my issue. But a dev/ expert can confirm.
I tried following steps outlined by rrobgill but didn't work for me. Let me know if I should upload run a new token:
If you could please try the following steps:
Restore /etc/resolve.conf to its initial default state - contains:
nameserver 127.0.0.1
Check that /etc/systemd/resolved.conf contains
DNSStubHandler=no
Force a reload of all of systemd-resolved's configuration files
sudo systemctl reload-or-restart systemd-resolved
Repair Pi-hole (to ensure dnsmasq's config files are correct)
pihole -r
Then, if you could please report the output of
systemctl status dnsmasq.service systemd-resolved
Should they not both be running:
if you could please try:
sudo systemctl daemon-reload
then once again
pihole -r
and once again, please report the output of
systemctl status dnsmasq.service systemd-resolved