We recently converted our navigation out of javascript because the search engines were not accessing all our pages. Now, several weeks later, the Google bot is visiting us but still not picking up our internal pages (non dynamic). Any ideas? Plus, Google is indexing pages that are no longer on our server. How can we fix this?

Many thanks!

Have you tried google Site Map ... and also site map within your site ... and have those pages that are not there any more redirected to current relevant pages ... and some time it takes more than few weeks for SE to crawl the site completly.