Eoin,
The jfbcchannel.php file seems to work now, which is great.
As for the new 404 error, are you using a 3rd party SEF extension? If so, please configure it so it 'skips' JFBConnect SEF URLs. Both sh404SEF and AceSEF both have this ability, and I'm pretty sure others do as well, but each one is different on how you do it. Mainly, you want it to use the "Default Joomla Router" or something to that effect and not the SEF extension's router.
Hopefully that will fix the 404 error. If you re-enable the .htaccess file and the domain name is once again stripped though, I'm not sure what the cause of that would be. Let us know, and we'll try to help, but we've never heard of that before.
Finally, and unrelated to JFBConnect, your site is loading multiple files from non-secure websites (Google Fonts and AddThis are two quick examples). That's causing the 'padlock' to not appear green as it should and nullifies some of the reason for getting an SSL in the first place. Just wanted to let you know, but again, that's not a problem with JFBConnect.
Thanks,
Alex