All of your files for public viewing go inside of your public_html folder, but you will see them if you access your pages using the www.
Keep you cgi-bin. All the others are FrontPage Extension folders except the images and need to be deleted through the cpanel. Look for FrontPage Extensions at your cpanel and Uninstall them there.
Not after you uninstall FrontPage Extensions, except for what files may or may not be displayed through directory listing. I myself just deleted what was in the htaccess and aded my own code.