The annual conference of the Research Network Macroeconomic and Macroeconomic Policies in Berlin had two sessions dedicated to stock-flow models, plus other papers using this approach in other sessions.
The program is available here
Using FoF data
An excellent piece of analysis of Flow of Funds data at the Bank of England:
Richard Barwell and Oliver Burrows, “Growing fragilities? Balance sheets in The Great Moderation”, Financial Stability Paper No. 10 – April 2011