First, hooray for wired having a "full page" link, so I do not have to go through hoops to read the whole article.
Second, it was interesting to read. Very exciting with real FBI agents and such. I did not look, but do you know if they released all of Regan's ciphertexts for hobby cryptographers to decode? I might find the time to try to crack it myself
Neal Stephenson also uses various encryption methods in his book "Cryptonomicon" which I can highly recommend.