Not sure whats happening.
Running update-rc.d , which is intended for the sysv init system, used to be enough when I tested this.
I had a bunch of those messages but they were related to a missing proper upstart job so upstart conditions the sysv init.d script to be used for the upstart init system.
I moved my Pi-hole to a dedicated Pi1 with regular Raspbian in the mean time so its a bit hard to test for me currently.
Without the cron job, what were the outputs for the other two (ps -e & netstat) ?
And try 'sudo status pihole-FTL' ?
And did the update-rc.d command create the necessary old style sysv symlinks in below folder ?
ls -al /etc/rc2.d/
Ohw and upstart creates logs in the folder '/var/log/upstart/'.
you can check if pihole-FTL logs are created in that folder and you can view them with the 'zcat' command.
So, I removed the entry from my crontab where I started the service on boot and rebooted my xbian to check the output of the commands you asking for.
The good news are that now when I visit the admin panel of pihole it works and the status is Active.
The strange thing is the output of the above commands: