There may be a bigger problem with the configuration. The debug test queries the
dnsmasq process for some specific records that should return back the customization that Pi-hole does, however they are blank on your installation.
Pi-hole dnsmasq specific records lookups
Can you explain a little how you have the Pi-hole configured? I noticed you have port assignments in the
setupVars.conf for upstream DNS servers as well?
index.php looks to have been corrupted by something. There are a number of errors for the file