A wonderful read. I know a little bit about frequency analysis and was surprised to see how straightforward its application was (in theory). I'm even more surprised that after a decade of Google, that this approach wouldn't be one of the first things tried out given the length of the text. As the OP describes, it was a chance encounter at a conference that machine learning was finally introduced into the problem. Until that point, the linguist had been trying in vain to decipher the text...is there still such a gap between the researchers and the computational experts who know how to implement solutions?

* to put it in a less-polite way: how the F else would you solve a problem like this, with non-computational methods?