I've got a reasonably large site and want to know how I can do a sitewide check to figure out if my site is preforming to it's full SEO potential, and the navigation is sound.

There are plenty of free tools out there that can tell you relatively quickly what sections of your site might be needing some TLC.

Internal linking

If you haven't got a Google Webmaster Tools account yet, get one as soons as possible. You can log in here and see all the internal links to your pages, and understand on a more basic level what pages are favored and which are neglected by your internal linking strategy.

Check out SEO4Fun's FreePageRankBot to show you your internal link flow. (Setting up the account requires some preserverance.)

If you have a page that receives many external links, but equally sends many links to external websites, improve your internal linking to this page to keep the internal link flow nice and ballanced.

Extarnal links

Use a combination of Site Analytics and Google Webmaster Tools to find out which pages are pulling in external links, and how much. (If have no anlytics package yet, use Google Analytics for free. WARNING: although basic privacy assurances hold, the data available to you will also be available to Google on some level...)

If you have pages of low importance, but link to them frequently (e.g. T&C's, privacy policies, etc.), then utilize the "nofollow" tag.

Content optimization

If your site has frequent content updates, use Google's date based filters to identify new pages of low quality (in this case meaning with little to no content or containing large volumes of duplicated content...)

If a particular page is doing well in the search rankings, consider adding content to it to broaden the keyword phrases it appeals to.

User interaction

Use your Analytics tool to learn what your highest traffic and best converting pages, and focus more link equity on them.

Use tools like Google's Site Overlay to understand what links users are clicking on. Are these pages marketed well enough on your site?

Testing

Create several pages with slightly varying content, and analyze which one performs better (= ranks higher in the search engines and converts more efficiently). Drop the variations that under perform, and deepen your testing. (Google's multivariate testing is the free tool to consider here).