The comparison features in vB should show you all differences in the templates. The method that seems to work best for me is opening the 'Edit Template' link for the template I'm about to compare in a new tab/window, then open the 'View History' link in it's own tab/window. Choose the versions to compare, then you'll see the differences and be able to easily switch to the window you opened the 'Edit Template' link in and apply any changes. Be sure to note which version it shows for the New/Old buttons when you start to compare them since it usually shows my custom template as the newest one and the updated template as the old one (seems reversed to me).
Once you edit the template then the 'Customized Templates' message should disappear from that one as it assumes that you've modified the template to add the updated changes.
If you're just concerned with making sure the secuity token feature has been added, you can search the default templates for 'securitytoken' to see where that was added. That part just mostly involves adding the following hidden input field to any <form>'s in your templates:
<input type="hidden" name="securitytoken" value="$bbuserinfo[securitytoken]" />
You must not have been around in the days of vB 2, before the plugin system was added. Updates were a *real* pain back then.
I really wish that there was some automated way to morph in the new security stuff, without having to get into code up to my eyebrows.