Well ... no one responded to my question here, but it seems the problem has already corrected itself. Perhaps it just took 2-3 weeks for link juice to be properly attributed to the new location of the 301'd site and subpages. I'm not back 100% in terms of traffic yet, but I'm 80% there.
Actionable Ideas for an Effective Analytics Strategy
5/17/2012 How to evaluate and gain clarity on your goals surrounding your website's analytics. Mine your Google Analytics data with purpose.