To a certain extent, yes. The site will be very dynamic based around performance of particular pages of the site so this section is essentially to give some structure to the site. The pages will also be accessible through a categorisation section of the site also but most of the time they will be accessed through redirection from using certain keywords in the search function.  Its quite a tough one to explain without giving too much away!

Well it is the main mechanism to avoid orphaning any of these particular pages within the site as there are approximately 5000 of them. This A - Z is a section is not a map of the entire site but just one section of it, so I think that all pages will need to be linked to as they are, in essence, priority pages of the site in terms of SEO.

Im creating an a to z type directory of internal pages within a site of mine however there are cases where there are over 500 links within the pages. I intend to use pagination (rel=next/prev) to avoid too many links on the page but am worried about indexation issues. should I be worried?"