/web/cgi-bin/php5 "$HOME/html/my/ow_cron/run.php"
by using the godaddy browse button to find the run.php
frequency is set to hourly
minute is set to x:05
It seems to be sending me regular emails on the hour so i guess its working
What is the username? my godaddy username? the one i use to login to godaddy
Yes, that's right if you have shared hosting and cPanel.
"$HOME/html/my/ow_cron/run.php"
Not sure about that path, not sure what the /my/ is about? Godaddy must use some non standard directory structure. Normally it's /home/yourusername/public_html/ followed by whatever folder/addon domain you decided to install in.
Have you tried third party cron job service like https://www.easycron.com? It allows setting up cron jobs that run every minute.
As you said you get the e-mail but it was received within an hour. This means that all notifications/updates of the user activity/mass mailing will be received by your users within an hour, if you're fine with that, then leave it at that.
As to the FTP problems you have, can you please provide more details on the issue?