google search only returns the pages that are in google's index, i believe. installing the custom search doesn't make them spider it anymore than they normally would. that was a deal breaker for me, because my site is thousands of pages and half of them might drop out of the search making it look like they don't exist.
there's an open source script that's been around for years, called "sphider". that's what i've been using. you'll need a database to install it, but it can spider you whole site and even has a few logs so you can see what's being searched for. the templates are totally customisable too.