The Like and Comment box are displayed below every articles because of the JFBConnect Content plugin. You can either disable this plugin entirely if you don't want them displayed. Alternatively, in the "Social" tab of the JFBConnect Admin area, you can configure what types of article views (article, blog, section, etc) and where (top/bottom) the Like and/or Comment box is displayed.
As for the registration error, can you tell us what the error is? That will help us determine a solution. Also, please make sure you've enabled the JFBConnect System and JFBConnect Authentication plugins.
Finally, if you can post (or private message us) your URL, that will help us see if there are any obvious configuration issues.
Thanks!
Alex