Different Types of Complicated Documents/Reports

I've been searching for a solution but haven't come up with any solid ideas/answers.

I'm trying to create the display of around 100 different reports. The problem is the reports don't follow a standard structure. I've tried and had limited success with epublish (http://drupal.org/project/epublish). Most of them have a Table of Contents main page that provides links of each sub item. Within sub items, there should be navigation links to the Prev, Table of Contents, and Next sub items.

Sorry for the long list, just trying to show all of the variety. I am working with the content people to standardize as much as possible, but most of the way these are done is required by the people who funded each report.

Links to the live (out dated) site:

• http://tmip.tamu.edu/clearinghouse/docs/abtf/
  Different authors of different reports, this I've actually duplicated using epublish
• http://tmip.tamu.edu/clearinghouse/docs/accounting/
  TOC with subgrouping
• http://tmip.tamu.edu/clearinghouse/docs/airquality/best/
  No TOC!
• http://tmip.tamu.edu/clearinghouse/docs/airquality/tdf/
  TOC, with list of Figures and list of Tables within whole report
• http://tmip.tamu.edu/clearinghouse/docs/alternate/sbcag/
  http://tmip.tamu.edu/clearinghouse/docs/general/hitf/
  TOC with sub items both in different ways
• http://tmip.tamu.edu/clearinghouse/docs/airquality/vsca/
  TOC with multiple levels
• and worst of all
  http://tmip.tamu.edu/clearinghouse/docs/general/sams/
  a TOC of different TOCs that contain multiple level links

Thanks for any help!