I figured out the answer here. This mailing list entry: http://lists.osgeo.org/pipermail/qgis-developer/2012-October/022627.html and this http://qt-project.org/doc/qt-5.0/qtcore/qsettings.html were helpful. I ended up going into the windows registry to figure out the names of the options (since that's where they're set when you use store QSettings natively in Windows. It was under HKEY_USERS/myid/Software/QuantumGIS. In there, I just experimented by turning things on and off to figure out what needed to be changed in the plugin. I did that like this.
settings = QSettings(QSettings.NativeFormat, QSettings.UserScope, 'QuantumGIS', 'QGis')
settings.setValue('/Projections/projectDefaultCrs', 'EPSG:2278')
Hope this helps someone else.