Actually, Ubuntu and Debian installation procedure is exactly same for Ajenti V. I've updated the article title to reflect that.

Please see the process log at /var/log/supervisor/process-name

/etc/nginx is automatically wiped & regenerated by Ajenti V when saving website configuration. Please store the certificates in a different directory.

This issue is now tracked at https://github.com/Eugeny/ajenti/issues/532#issuecomment-58726778

But your previous commands' output show that /usr/local/bin/ajenti-panel exists and is executable. How can this be?

Looks like /usr/local/bin isn't on your $PATH.
If you're currently in /usr/local/bin, you need to execute: ./ajenti-panel

So... have you tried running ajenti-panel? It should start the panel in foreground mode (for testing). If that works fine, go ahead and start it as a service using the rc.d script you have downloaded.

This means that some other process has taken the port 8008 

Hi Joey,

Please check that your date & time settings are correct - this is the most often cause of SSL failures.