CTC has now released a report based on the documents provided at the link in my earlier post:
The Combating Terrorism Center at West Point is pleased to present the report, Cracks in the Foundation: Leadership Schisms in al-Qa’ida from 1989-2006. Based on a collection of al-Qa’ida documents recently released from the Department of Defense's Harmony Database, in addition to the previously released documents utilized in the Combating Terorrism Center’s two prior Harmony reports, this report analyzes the history of al-Qa’ida’s internal and long-running debates over the strategies and larger goals of the jihadi movement. Many of these documents, captured in the course of operations supporting the Global War on Terror, have never before been available to the academic and policy community. Cracks in the Foundation includes a richly sourced account of the ongoing struggle between different factions among al-Qa’ida’s leaders and specific recommendations for effectively exploiting weaknesses arising from these internal struggles. We have provided brief summaries of each of the released documents, and the full texts of the released documents can be accessed via hyperlinks within the report, both in their original Arabic and in English. We hope this report will serve as a useful resource in our collective efforts to better understand and combat al-Qa'ida and its affiliated movements.
Cracks in the Foundation: Leadership Schisms in al-Qa’ida from 1989-2006

For those who don't feel like slogging through the entire 78 page pdf at once, CTC was thoughtful enough to break it down so you could access it in chunks:

Foreword

Introduction

Part I
1990-1996: Al-Qa’ida in Afghanistan, Sudan and Somalia


Part II
1996-2001: The Taliban Refuge and the War with America


Part III
2001-2006: Dispersal, Reconsolidation and Problems in Iraq


Conclusion