Good to hear you got it all running.
Coincidentally today, I was looking for the thread size of the VC bolts and I stumbled upon this post from a decade ago:
http://intellidog.com/dieselmann/idi2.htm
He discusses this in a section titled:
Engine stalls at stops or when deprsessing clutch
"Stalls returning to idle after snapping throttle open. Injection pump problem caused by poor quality or contaminated fuel. Check for presence of water in the fuel--removal of the injection pump governer cover may be necessary to find contamination, but is not advisable unless you have experience. Check idle speed setting and injection pump timing, as well as cold timing advance--timing should advance at least 2 degrees with 12 volts applied to the rear solenoid terminal. Adding Stanadyne's All Season Diesel Fuel Conditioner may cure this problem, but if it persists, or if there is no cold advance, replace the injection pump. Recommend that the Stanadyne All Season Fuel Conditioner be used periodically to prolong injection pump life."
Since you have already solved your problem this is kind of not important, but if someone reading this thread in the future ran into a similar clutch issue, this link might be interesting.