In order to secure the connection between WHMCS and FreeNAS, it is recommended to install an SSL certificate on the FreeNAS server. Under System -> General an SSL certificate can be installed.
This SSL Certificate can then be used to provide SSL secured FTP access (FTP over SSL): http://doc.freenas.org/9.3/freenas_services.html#encrypting-ftp
You may want to customize welcome messages for SSH and FTP to reflect your company name instead of FreeNAS.
- The MOTD SSH banner can be adjusted at System→ Advanced
- The FTP login message can be adjusted at Services → Control Services → FTP wrench icon → Advanced Mode → Display Login
- The changes for Samba and iSCSI was already carried out at the configuration steps of the services.
After a configuration change has been made, the corresponding service must be restarted. The restart is done in the menu Control Services.