There are various things to say, Jim, but mainly:
1) It probably makes more sense to focus on this paper:
* Josef Ludescher, Avi Gozolchiani, Mikhail I. Bogachev, Armin Bunde, Shlomo Havlin, and Hans Joachim Schellnhuber, [Improved El Niño forecasting by cooperativity detection](http://www.pnas.org/content/early/2013/06/26/1309353110.full.pdf+html),
_Proceedings of the National Academy of Sciences_, 30 May 2013.
It seems to have a simpler and more reasonable methodology than this earlier one:
* K. Yamasaki, A. Gozolchiani, and S. Havlin, [Climate networks around the globe are significantly effected by El Niño](http://arxiv.org/abs/0804.1374), April 2008.
2) I have the strong feeling that people in this subject - "climate network theory" - are just messing around trying to see what works. The definitions of various quantities are a bit _ad hoc_, not justified by deep reasoning. This is good because it means we can mess around a bit ourselves, and try to do something that works better. But it means we can't just learn the stuff by reading papers and trusting them.