In the Excel spreadsheet below, you'll find a comparison of the Beale cipher numbers and those found in the Hart Papers. There are 6 differences between the two for Ciphers #1 and #3, but there are 142 differences between the Beale and Hart numbers for Cipher #2 (the only cipher to have been solved).
Also all of the ciphers have been decoded using the method to solve Cipher #2. In Cipher #1, you will see the Gillogly strings highlighted in bold.
Jeff Alexander sent me a link to his page which contains a very useful Beale Cipher decoder for ciphers #1 and #3. Go give it a try!
Ron Gervais sent me a link to his page which contains very useful analysis on the Beale Ciphers. As well as a very powerful piece of software (available for free) that will allow you to decode any document against any of the ciphers.
More information will be coming soon. Including some analysis on letter frequency.