Have you created and submitted a XML sitemap to google through webmaster tools?
Also, Seomoz recommends limiting the links on any page to less than 100. The reason they state is "When search engine spiders crawl the Internet they are limited by technology resources and are only able to crawl a certain number of links per webpage...though if your pages have a high page authority, search engines will usually follow more links."
With this in mind I would consider building links to deeper pages on your site to help build authority and help google find some of these pages that aren't indexed.