We too were on this road last year (2010).
The Zorkul area is a natural park, but you can get the permit easily in Khorog. We asked at pecta, and the lady from the zapovednik administration even drove to the pectad infromation center (as her office seams to be a bit outside), to give us the permit.
The problem in Khargush was, that we were ok with the permit for the natural park, but the military wanted something more (2 years ago , they only wanted the propusk for the park). After some discussions, we could pass. There is another military post at the other end (after Zorkul).
As rivers were high, when we were in the region, we took the road from Djarty Gumbaz out to the M51 (near Karasu). The road was ok and no bad river crossings (we were on bikes).
Our pictures of Zorkul region are here: Kurze Sommertour durch Mittelasien: An der afghanischen Grenze entlang durch den Zor Kul Nationalpark
Concerning the GBAO, we had problems when driving up the Shuqdara Valley, in fact this district was not listed on our GBAO stamp (done by Vienna consulate), but after some long lunch, we could continue our journey.
Kind regards
Christian
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