Bill,
I have to strongly disagree. Firstly, the use of automated "seo" software to analyze sites is rarely advisable. There are too many factors that can't be gauged by software, and too much emphasis is placed on very outdated factors like densities and frequencies. These software packages have been relatively ineffective since about 2003 or so, and are universally panned in the professional SEO community.
One of the biggest flaws, in my personal view, is that they place too much emphasis on one keyphrase and the site homepage. Traffic now comes from hundreds of keyphrases (see
Long Tail) and enters your site any just about any page. This is the reality of modern search.
Regarding the value of links - nothing will influence the big 3 search engines more than links and anchor text (see
Google Bomb). It's possible to rank highly for terms that aren't even on your page, as long as the links tell the engines that your page is relevant to that term. While Google has claimed they have minimized the effect of Google Bombs, the reality is that link anchor text still rules the day.
Ryan