A few weeks ago I received an email from a Finnish math student who claimed that, analyzing the Exhibit 2 and 3 material on the National Cryptologic Museum web site and The Chaocipher Clearing House, he was able to determine how Chaocipher Exhibits 2 and 3 were enciphered. To prove his claims he submitted a two-page document.
It did not take too long for me to verify that he indeed had solved the exhibits. You can find his document and other material on The Chaocipher Clearing House.
The paper is a bit sparse in places and could use some elucidation by the members, but it's all there and is spot on.
With this paper it seems that all five Chaocipher exhibits have been deciphered and figured out. There is still more Chaocipher-related research to do (I hope to post an entry on the many areas remaining) but in terms of the exhibits we can rest easy now.