Hi Kit2,
Incase you are still working on this, here is the solution that worked for me.
For whatever reason, I cannot get pihole to work on anything other than port 80, even though I really want apache on that port, and need port 80 open to configure ssl with lets encrypt.
I ended up temporarliy switching pihole/lighttpd to any port (I used 81) and then configuring ssl.
Once this was done I put pihole/lighttpd back on port 80, and apache on port 81. To make apache work cleanly and not open my pihole up to the web I forwarded external port 80 to internal port 81 on my router.
Hope this helps!