main.custom.conf

location ~ \.php$ {
  include       fastcgi_params;
  fastcgi_index index.php;
  fastcgi_param SCRIPT_FILENAME $document_root$fastcgi_script_name;

  fastcgi_pass  127.0.0.1:12345;

  # Prevent arbitrary code execution by third parties with
  # try_files directive.
  # http://wiki.nginx.org/Pitfalls#Passing_Uncontrolled_Requests_to_PHP
  try_files     $uri =404;

  location ~ /wp-admin {
    include       fastcgi_params;
    fastcgi_keep_conn on;
    fastcgi_pass  127.0.0.1:9000;

    try_files     $uri =404;
  }
}

How did you come up with the actual value for 12345 in the first fastcgi_pass? I can't find anything in any tut that says anything except 9000, which you have second.