Regarding the similar distribution you pointed out in the plot, I was considering that perhaps the cipher numbers were ordered in a gridlike fashion on the original, such that perhaps vertical or diagonal reading, or more exact positioning would reveal extra information.

So I was browsing the NSA pdf files "The Beale Papers" from archive.org, and apperently according to these files theres even different versions of the CIPHERTEXTS!

It is unclear to me why there would be different ciphertexts floating around, possibly:

1) the pamphlet author published multiple versions 2) after analysis, later authors "fixed" the ciphertexts as opposed to describing the encryption errors in the decoding mechanism 3) flat out disinformation by: the publisher (how does the anonymous author defend the true ciphertext? would other publishers at the time dare to publish a second version of the cipher? how does this author prove he is the same anonymous person?), disinformation by treasure hunters (you can recognnize your own manipulation, but this confuses everyone else)

Do we know what happened with the publisher? did it merge with others, and is it still in existence under a new name? Do they perhaps have any early original (from the box, or original manuscript from the anonymous person, etc...)