So for the type work I do, I pretty much ignore most tags. I'm only concerned with the text and it's data. So, for your transcription I did the following:
For all of those, I converted them to spaces. If that's not the intended interpretation of the breaks, let me know and I can rework it.
? - splats. While I could make some educated guesses as to what splats might be, I strip any word that contains even 1 splat. I'm interested in letter transition accuracy which shouldn't change with splat removal.
You also use b, j, u and v. I included them. In this ledger build I used words length 3+ and considered rare words to be count 3-. Your b only occurs as a suffix therefore, it has no midfix or suffixes that appear after it. And your u has only one occurrence as tauiin where it's a midfix so it only has a rare i as a midfix that follows it. All other occurrences are as suffix. That's why those two letter rows will look a bit empty.
Also for my work, I've created a 'mappings' JSON file that I work with. It basically breaks the Voynich down into it's unique words and then records a good bit of data about each word. I've included it for you to look over.
| Prefix | Core midfix | Rare midfix | Suffix |
|---|
| a | i, l, r | a, c, ch, d, e, g, j, m, n, o, s, sh, u, x, y | ch, d, e, g, i, j, l, m, n, o, r, s, y |
| o | a, ch, d, e, i, l, o, r, s, sh | c, g, h, j, m, q, x, y | a, c, ch, d, e, g, j, l, m, n, o, r, s, sh, y |
| d | a, ch, e, o, sh | c, d, g, i, l, r, s, x, y | a, c, ch, d, e, g, l, m, o, r, s, sh, u, y |
| l | a, ch, d, o, sh | c, e, g, i, l, q, r, s, x, y | a, c, ch, d, e, g, l, m, o, r, s, sh, y |
| ch | a, d, e, o | c, ch, g, h, i, l, r, s, sh, y | a, b, c, ch, d, e, g, h, i, l, m, o, r, s, sh, x, y |
| sh | a, ch, d, e, o | c, h, l, s, sh, x, y | a, d, e, l, o, r, s, x, y |
| e | a, d, e, o, s | c, ch, g, i, l, r, sh, y | a, b, c, ch, d, e, g, l, m, n, o, r, s, sh, u, y |
| y | a, ch, d, sh | e, h, i, l, o, q, r, s, y | a, ch, d, e, g, l, m, o, r, s, sh, u, y |
| s | a, ch, o, sh | d, e, l, q, r, s, y | a, ch, d, e, g, i, l, m, n, o, s, y |
| r | a, ch, i, o, sh | d, e, l, x, y | a, ch, d, e, g, i, l, m, o, s, y |
| q | o | a, ch, e, r, s, y | e, o |
| h | none | a, ch, d, e, h, o | d, o, y |
| m | none | a, ch, d, o, sh | d, g, o, y |
| n | none | a, ch, d, o, sh, y | d, e, g, l, o, r, s, y |
| g | none | a | o, s, y |
| x | a | d, o | y |
| c | none | a, ch, e, o, s | o, y |
| i | d, i, n, r | a, c, ch, e, j, l, m, o, s, sh | ch, d, g, i, l, m, n, r, s, x, y |
| b | none | none | none |
| j | none | a, sh | y |
| u | none | i | none |
| Prefix | Core midfix | Rare midfix | Suffix |
|---|
| a | i, l, r | a, c, ch, d, e, f, g, j, k, m, n, o, p, s, sh, t, u, x, y | d, e, g, i, j, l, m, n, o, p, r, s, y |
| o | a, ch, d, e, i, l, o, r, s, sh | c, f, g, h, j, k, m, p, q, t, x, y | a, c, ch, d, e, f, g, j, k, l, m, n, o, p, r, s, sh, t, y |
| d | a, ch, e, o, sh | c, d, g, i, k, l, p, r, s, t, x, y | a, ch, d, e, g, l, m, o, r, s, sh, u, y |
| l | a, ch, d, o, sh | c, e, f, g, k, l, p, q, r, s, t, x, y | a, ch, d, f, g, k, l, m, o, p, r, s, sh, t, y |
| ch | a, d, e, o | c, ch, f, g, h, i, k, l, p, r, s, sh, t, y | a, b, d, e, g, i, k, l, m, o, p, r, s, sh, t, x, y |
| sh | a, ch, d, e, o | c, f, h, k, l, s, sh, t, x, y | a, d, e, l, o, r, s, x, y |
| e | a, d, e, o, s | c, ch, f, g, i, k, l, p, r, sh, t, y | a, b, ch, d, e, f, g, k, l, m, n, o, p, r, s, sh, t, u, y |
| y | a, ch, d, sh | c, e, f, h, k, l, o, p, q, r, s, t | d, f, g, k, l, m, o, r, s, t |
| s | a, ch, o, sh | c, d, e, f, k, l, p, q, r, s, t, y | a, d, e, g, i, l, m, n, o, s, y |
| r | a, ch, i, o, sh | c, d, e, f, k, l, p, x, y | a, ch, d, e, g, i, k, l, m, o, s, y |
| q | o | a, c, ch, e, f, k, p, r, s, y | o |
| h | none | a, c, ch, d, e, h, k, l, o, r, s, t, y | d, e, h, o, s, y |
| m | none | a, ch, d, o, sh | d, g, o, y |
| n | none | a, ch, d, k, o, sh, y | d, e, g, l, o, r, s, y |
| g | none | a | o, s, y |
| x | a | d, o | y |
| c | none | c, f, k, p, s, t | f, t, y |
| i | d, i, n, r | a, c, ch, e, f, j, k, l, m, o, p, s, sh, t | ch, d, g, i, l, m, n, p, r, s, x, y |
| b | none | none | none |
| f | none | a, ch, d, e, h, o, s, sh, y | o, y |
| j | none | a, k | y |
| k | none | a, c, ch, d, e, h, i, l, o, s, sh, y | a, ch, d, e, g, h, l, o, r, sh, u, y |
| p | none | a, ch, d, e, h, o, p, s, sh, y | a, ch, o, s, y |
| t | none | a, c, ch, d, e, h, i, k, l, o, sh, y | a, ch, e, h, l, o, s, sh, y |
| u | none | i | none |
I wasn't able to attach the full gallows file as even zipped it exceeded the 2mb limit. I got it down to size with other formats but the forum rejected them. Sorry.
With gallows intact, standalone c mostly transitions into f/k/p/t. In 98.1% of those token occurrences, the gallows is immediately followed by h, so the pattern is: c + gallows + h. When the gallows is stripped, those forms collapse to atomic ch , which is why the c row changes so dramatically.
There are 217 c-initial types in the transcription, 896 tokens, and every one has a gallows. After stripping, 871 of those 896 tokens become ch-initial. Outside gallows words, I find only one minimum-length-3 word in your transcription containing standalone c: ocsesy.
So the main result is in your transcription, standalone c is overwhelmingly tied to gallows constructions, especially c + gallows + h.