Jep, for LetsEncrypt you need to switch back. However is port 443 used by another service on the same server machine? Otherwise it would be easier to keep the webserver listen on port 443 but forward 4443 from router to 443 on server?
However, if you can’t find the config files:
Are you sure that Apache ist your webserver? By default, if you did not select a different choice, Lighttpd is installed, with config file /etc/lighttpd/lighttpd.conf. Port change should be trivial there.
/var/www/nextcloud/config/config.php however must exist, if Nextcloud is running. Probably some typo when searching for it?
Hmm, you restarted Lighttpd? Also check: journalctl -u lighttpd or /var/log/lighttpd/ for logs. Especially if it started up successfully and some line that states that it listens to port 4443 (should be inside somewhere, AFAIK).