This is normal with Pi-Hole V4 - dnsmasq is embedded in pihole-FTL and pihole-FTL runs on port 53 in place of dnsmasq. All the functionality and configuration remains the same. A debug log will report dnsmasq as "failed" or "inactive". Your log reports it as inactive.
*** [ DIAGNOSING ]: Ports in use
...
*:53 pihole-FTL (IPv4)
*:53 pihole-FTL (IPv6)
*** [ DIAGNOSING ]: Pi-hole processes
[✗] dnsmasq daemon is inactive
You can ignore the errors on 11/11/2018 regarding php-cgi not loading, that has been resolved. Currently I am not seeing any errors (or any output) in the /var/log/lighttpd/error.log. No worries, I understand time. Thanks!
Additional information: If I attempt a "git checkout master", my machine locks hard at the step where it verifies the MD5 of FTL. Unresponsive on console, CPU maxed at 100%. I left it running that way for approx 12 hours before hard booting. This is with Xeon 5550 2.67Ghz CPU. Comes back up with the same symptoms, pihole is working, I can see pihole.log adding entries, but nothing in GUI. Thanks!
2018-11-11 15:33:31: (mod_fastcgi.c.1478) invalid "bin-path" => "/usr/bin/php-cgi" (check that file exists, >is regular file, and is executable by lighttpd)
2018-11-11 15:33:31: (mod_fastcgi.c.1159) the fastcgi-backend /usr/bin/php-cgi failed to start:
2018-11-11 15:33:31: (mod_fastcgi.c.1163) child exited with status 2 /usr/bin/php-cgi
2018-11-11 15:33:31: (mod_fastcgi.c.1166) If you're trying to run your app as a FastCGI backend, make >sure you're using the FastCGI-enabled version.
If this is PHP on Gentoo, add 'fastcgi' to the USE flags.
2018-11-11 15:33:31: (mod_fastcgi.c.1518) [ERROR]: spawning fcgi failed.
2018-11-11 15:33:31: (server.c.1269) Configuration of plugins failed. Going down.
Your PHP install is either broken or the lighttpd PHP config is misconfigured. Check that you have a FastCGI compatible version of PHP installed, and that the path shown above is valid.