1. The search form is editable here:
Search Form (searchform.php) and by CSS
2. If you mean the links wordpress adds automatically when you add a page it is listed as a list via the wp_list_pages function. Usually located in the sidebar.php file if you are using the default theme.
3. Your plugins a lot of the time contain there own CSS file. If they haven’t come with one you can go to your website and view the HTML output source and find out what classes are attached to these plugins HTML. From there you just go into your stylesheet and add the classes and ids and style them appropiately.