What kind of ranking are you referring to, Alexa?

Where are you getting your information? Not sure what you mean by "ranking," but Alexa and similar sites all have issues with their data- take with a grain of salt. I assume you mean TBPR (tool bar page rank) for PR? Again, take with a grain of salt. Where are you getting the numbers of incoming links? The link: function on Google has never been reliable (for one of my site, Google shows a few thousand links, while Yahoo shows over 25,000).

There are many factors in Google's algorithm. Besides just the number of links, Google also looks at quality. Age of domain is another factor. Oh, did I mention the actual content on the site?

When I say ranking I mean traffic rank and when I say PR I mean google Page Rank (grey bar). My point is I have much more links linking to my site and they are on page 1 while I am on page 3

When I say ranking I mean traffic rank

Again, according to whom? There are many sites that show "traffic rank" statistics. As previously advised, take each with a grain of salt.

when I say PR I mean google Page Rank (grey bar)

See my point about TBPR.

My point is I have much more links linking to my site and they are on page 1 while I am on page 3

And see my point about links being only one component of Google's algorithm.

Alexa for traffic rank. Quality is there. Age: About 10 years. Content is more than there.

One more question:

On my site I have cold fusion pages (about 10 cfm pages) as well as htm pages (about 30 htm pages). The cold fusion is used for my online store. The htm pages are information based. Recently I decided to focus more on the store aspect and remove most of the htm pages. Just keeping the "privacy" "about us" "contact us" "testimonials" pages. So I excluded them from my navigation. These pages were indexed by google however. How does this affect my site? Will google assume that my navigation is bad as I do not link to these htm pages anymore and thereby drop my rankings? How should I remove these pages without being hurt by google? And if so since I am removing content from my site will this hurt my rankings even more? Or will my site be helped due to the fact that it will be easier to navigate etc.?

The htm pages are information based. Recently I decided to focus more on the store aspect and remove most of the htm pages.

This is just my opinion, but removing content was the wrong direction to go in.

I realized but the information was alot. The navigation was not well done and the information was distracting to the store. The company is a brand! I just want to know how to remove these htm pages? If to just remove them from the nav? Or delete them? Or what?

Were the .htm pages ranking for anything? If so it makes sense to keep them from a traffic perspective.

If you want to remove them, then remove them from the nav and delete them. You could also use a 301 redirect to redirect them to an appropriate page.