zach,
it is an issue in the creation of the netCDF file not the extraction.
when you write successive variables to a netCDF file, a temp file is
created in which the current file is copied over too. This copy and recopy
takes progressivley a large amount of time.
here is a web page that explains this:
http://www.cgd.ucar.edu/csm/support/FH/speed.shtml
you may be experiencing slow down from the grib read as well, so there
could be two factors against you.
you may want to pre-define the file size etc. this can help with speed:
http://www.cgd.ucar.edu/csm/support/FH/method_2.shtml
sm
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