I found my server was missing all files within the /usr/local/cpanel/src/templates/ folder.
These would include:
/usr/local/cpanel/src/templates/apache1/ssl_vhost.default
/usr/local/cpanel/src/templates/apache1/vhost.default
/usr/local/cpanel/src/templates/mainacct_mailbox_size_warning/main.default
/usr/local/cpanel/src/templates/mailbox_size_warning/main.default
/usr/local/cpanel/src/templates/mainacct_disk_warning/main.default
/usr/local/cpanel/src/templates/apache2/ssl_vhost.default
/usr/local/cpanel/src/templates/apache2/vhost.default
/usr/local/cpanel/src/templates/bandwidth_limit/main.default
/usr/local/cpanel/src/templates/admin_bandwidth_limit/main.default
/usr/local/cpanel/src/templates/admin_disk_warning/main.default
/usr/local/cpanel/src/templates/mainacct_emailquota_notifylist/main.default
These files are email templates.
I have no idea how to fix this, I was able to copy the files from another server.