So a site I SEO'ed is taking too long to rank high, although I compared vs the site that rank #1 and #2 with the keywords I have and found that my prominence and density are higher that other sites.

I also found this, only two of my pages are indexed: using google site:www.weburl.com

I also found that google only mentions 6 sites that backlink to my site, where I know at least 5 more are missing.

Not to mention that the site had over 250 broken links and the previous webmaster still submitted the site to SE.

OK, now what, I thought what if I redesing some of the pages, rename them and resubmit them, I mean, make significant changes, and since like I notices, none of my pages are really indexed but 2.

Also, should I resubmit the pages that are not indexed??

Any suggestions??

Don't resubmit to change your pages. Resubmitting won't do anything for you. Once a page on your site has been indexed the search engines will follow the links on that page and index the rest. In Google's case they often limit the number of pages they index for sites based on a criteria not yet determined by outsiders. All you can do is wait it out and continue to implement an SEO strategy (i.e. continue to add quality content and seek incoming links).

You may also want to submit a sitemap... here is an easy sitemap generator for google...
http://www.auditmypc.com/free-sitemap-generator.asp
You can resubmit that each time you change something on your site...

You don't actually have to resubmit it. Google will continually pull down that sitemap so all you need to do is update whenever you make a change. Ideally you can create a dynamic sitemap with PHP which automatically updates itself for you.