I have a site with a simlar URL setup as http://www.agcdirectory.org My site only has 20 pages index in google but there are 1000's of pages. Is my main issue the dynamic URL's
Last time I knew, the google spider would not follow links within a javascript drop down menu. The sitemap you have in your footer is also for agc.org, not agcdirectory.org, and that site is well indexed by Google. Try creating a site map page like you have for agc.org for agcdirectory.org and link to that from within your site.
you can go through url rewriting o you can go through site map, both are new updates in search engine optimization, If you can go through url rewriting then it's take time because it's related to coding part instead of that if you can go through site map, which is very simple and easy to index you all pages in major search engines,but make sure that your site map must be in paging wise.