Meg,
We separated Kay's QL=3 into 3 (bad retrieval), and 4 (non-retrieval). Otherwise, the QLs and quality algorithms were defined by Kay and they have not significantly changed since 2006. I wrote the document you reference based on Miami's code, as I was porting it to the OBPG environment. There's a bit more on the Miami vs OBPG transition here, that may help:
http://oceancolor.gsfc.nasa.gov/DOCS/modis_sst/sst_transition.htmlNote that Peter Minnett and Bob Evans at Miami are still responsible for the MODIS SST algorithm and quality screening. We just implement and process. If you want to be sure, you can also look at the code (sst.c) that is in SeaDAS.
-- bryan