Hi James,
Once you have a list of pages that are returning the 404 error, you just need to setup 301 redirects to the correct page for each broken link. A 301 redirect is a permanent redirection, telling search engines that the page no longer exists, and it should point all visitors (and link juice!) to the new location that you specify.
The easiest way to do this is via FTP. You can edit your .htaccess file on your server by simply adding the following code:
Redirect 301 /oldpage.html http://www.yourwebsite.com/correctpage.html
...you'll need one of those lines for each page that is 404'ing. This should go at the top of your .htaccess file, and should be one line for each error.
Hope that helps!