I got rid of the trace bar at the bottom, and I've solved the issue that caused the extra navigation bar at the side. The 'edit' boxes that were appearing on the main page appear whenever you use more than one heading on a page. I just moved everything on the first page into a table and that has got rid of those.
Other than that the wiki is now ready to be populated. If anyone has any comments on the wiki send them my way - otherwise I will leave it as it is for people to use.