One of the major figures in the early 20th century history of the Voynich Manuscript was John Matthews Manly, the man who definitively debunked Newbold's strange micrographic cipher claims. During the First World War, Manly worked in the US Military Intelligence Division, and left in 1919 having attained the rank of Major. After that, he put most of his time at the University of Chicago into researching Chaucer, before dying in 1940.
Interestingly, Manly's papers are held by the University of Chicago: there's even an online guide to them, which lists a whole set of Voynich & non-Army cryptographic folders to look at, particularly in Boxes 4 and 5. One day, if I happen to get the opportunity to spend a day in Chicago, I'd love to go through these: Manly was a smart guy, so it would be fascinating to find out what was going through his mind (however indirectly).
Folder: 19 - Table of Latin Syllables
Folder: 20-21 - Photographs of Voynich Ms
Folder: 22 - "Key to the Library" (JMM's?)
Folder: 1 - Worksheets
Folder: 2 - Photographs of Mss (Including Français 24306, incomplete) and of one printed label
Folder: 3 - Three working notebooks, labelled "Bacon Cipher"
Folder: 4 - Notes on code for article; other notes on Sloane 830 ["Written in the years 1575-6, by a person whose initials appear to be M.A.B.", according to levity.com] and 414 [two collections of "chymical receipts"]
Folder: 5 - Worksheets on related ciphers: "Galen's Anatomy" [?] and "Kazwini" [presumably the 13th century Persian astronomical writer Al Kazwini]
Folder: 6 - Articles on the Voynich Roger Bacon Ms
Folder: 7-8 - Notes: ciphers in other Mss; other notes on printed sources
Folder: 9 - Notes on alchemical Mss, etc.
Folder: 10 - Notes for Bacon Cipher; "Key to Aggas"
Folder: 11 - Notes on texts in cryptography
Folder: 12 - Miscellaneous notes and worksheets
Folder: 13 - Bibliographies
Folder: 14 - Photostats of Mss: John Dee (Sloane 3188, 3189, 2599): unidentified
Folder: 15 - Notes on Vatican Latin Ms 3102 [Here's the Jordanus page on this ms, Manly reproduced f27r in his article, while Newbold's book reproduced f27r and f27v opposite p.148 and p.150]
Folder: 16 - "Notes on an Inquiry into the Validity of the Baconian Bi-Literal Cypher for the Interpretation of Certain Writings Claimed for Francis Bacon"
Folder: 17 - Comments on "Sixty Drops of Laudanum," by E.A. Poe
Folder: 18-19 - "The Bi-formed Alphabet Classifier" of the Riverbank Laboratories
Folder: 20 - Notes on Shakespeare/Bacon cipher
Folder: 9 "Roger Bacon and the Voynich Ms" by JMM, reprint [first page is here on JSTOR]