AREU, 16 Jan 12: Thirty Years of Conflict: Drivers of Anti-Government Mobilisation in Afghanistan 1978-2011

PRIO, 1 Jan 10: Understanding Warlordism: Three Biographies from Afghanistan's Southeastern Areas

Also from 2010, CPAU's Conflict Analysis of Badakhshan, Kunduz, and Wardak.

A bit older, but still useful, from the Konrad Adenauer Foundation: Islamists, Leftists – and a Void in the Center. Afghanistan's Political Parties and Where They Come From (1902-2006)

And if you can get a hold of the Open Source Center's "Master Narratives" paper on Afghanistan, that is also a useful read.

Finally, another good read is David Edwards' Before Taliban: Genealogies of the Afghan Jihad