Related to the simulation, all of the page content is present including the links. The site is ColdFusion - I have CF sites with gt 500 pages deep which I have had no issue. There are three sets of links on each page, a list-menu set (Suckerfish) at the top, a plain text set contained within the body content, and an included set provided by include through custom tag (also have not experienced issue previously). Actually, all of the text content found in the custom tag appears in the simulation output, as a matter of fact the simulation shows all three sets of links as mentioned above, so regardless of static or include the links are present in the simulation?
Below the page layout section all of the site's links, both internal and external are identified.
The Google cache is showing the previous site. New site propagated on Monday the 12th, so Google has not even crawled yet.
Ok, just ran the tool again and Success - Call me crazy but maybe I tried too early and the tool was trying to access the old domain server which was a .swf site and would only be recognized as one page.
-Issue Resolved- Lesson learned - Wait one additional day after propagation to run the sitemap generator tool.
Thank you for looking at that!