I've been following this thread excitedly since I finished the book on Saturday. This thing is a real stumper.
I've seen this mentioned several times, so I dumped the high res picture into the GIMP and played with the Brightness (he he he...) and contrast levels.
Here's what I get:
It doesn't seem like she's referencing this Pattern as some sort of key, but as connected to the symbolheads (I think she only saw these in Kharbranth). I think this could mean Pattern and the symbol heads are related somehow, but I think it also means that Pattern isn't reminding her of a cipher (directly at least). I have questions about the symbol heads, but that's probably for another thread.
Other thoughts:
That chart on the Pallinaeum sounds promising, but I don't think we have access to it (do we?).
I liked the "The key is in the book" info. It sounds like it's either a book key or there's some sort of xor/addition in place that goes on (the latter would pretty much have to be the date string). The best candidate I see is fictional Words of Radiance - we have lost of chapter and page info about it, and Mr. T certainly could have known about it. Treating 10's as a single character gives 141 = 3*47 characters, which allows triplets, but isn't terribly promising.
Putting it in pairs and newlining every 11 pairs results in 12 34 being in the same place on lines 6 and 7 as well as 51 21 being in the same place on these same lines. The chi-2 for line pairs doing this gives p~.05, so it may or may not be random. If it is not random, the it suggests sentences of parallel structure to me.
Question's
1)What is Mr. T's goal in using this code? If it's to condense for efficiency, that's good, but it disallows things like needing to add or subtract a "key value" - that's needless obsfucation (and wastes his time).
2)Raising the question: Did Mr. T make the diagram? He doesn't remember doing so, though he claims to somewhat recognize the handwriting. If his advisers are evil, they easily may have let someone or something else produce the diagram on one of his bad days. Also, misleading statistical reasoning of his advisers not withstanding, the fact that it was such a massive outlier makes it suspect. I'm not sure how likely this is, but the answer changes that books/keys the author had access to and also their motivations.
EDIT: embarrassing typos, and I probably didn't get all of them....