It's been 13 years. Has there been any cryptoanalysis? I can't tell if the problem Paul Crowley found in http://www.ciphergoth.org/crypto/solitaire/ is sufficient to sink it.
Unless the data is random (which is to say the additional layer of crypto is probably not buying you much) you can do e.g. frequency analysis on the output of the cipher. If you have a reasonable sized corpus (given how biased the PRNG is, probably a few thousand characters is overkill) you can probably break it effortlessly.
I hadn't known that Bruce Schneier created Pontifex for the book as I didn't know who he was back in the 90's. Kinda neat to circle back to an old favorite and learn that someone with whom you've become familiar since the last read contributed a key plot point.
I remember writing the bulk of the Wikipedia article[1] on this cipher back in my late teens when I was getting into crypto. Checking back, it's been heavily edited, but it retains the bulk of the original structure and all of the original example that I used. Kinda neat.
I remember reading Cryptonomicon in high school, and being fascinated and terrified by the Perl implementation of this in the book. It was a perfectly rectangular, quarter page quote, with no spaces and a terrifying proliferation of sigils.
I bought a set of Dungeons and Dragons dice (the set that has dice ranging from 4 to 20 faces) and coded up a Lisp program that turned a roll of 5 of these dice (approx. 16.4 bits of information) into 16 bits (sometimes you have to re-roll). With four rolls I have enough data to seed Lisp's 64-bit PRNG, which was my goal. After all, I use (random x) a whole lot.
I'd love to see another pass at this. I've frequently got a deck of cards on me, and a 225 bit key isn't bad for a symmetric algorithm; the question is how to extract it smoothly and easily...