Voynichese is a numeric cipher?

[ololololo]

Your observations about words could well do with their own thread.
A quick check in Notepad++ on RF1b-er.txt for "ol.daiin" gives credence to this ngram-word unit appearing more often in the Herbal sections
with a second peak in the Pharma section and also a strong absence in the Balneo & Stars sections. Quite interesting, very well observed.

As for this thread, if you could give a clear walk-through example of how this numeric cipher would work, that would be most helpful.(to me at least)

I don't know for sure, and I can't say what kind of numerical code is used in the manuscript, but if it's a nomenclature code, it seems to be quite simple and doesn't contain any special words (this can be easily proven by breaking down any word into "letters"; in fact, this can make decryption more difficult, as nomenclature codes rely on specific words for decryption). 
To disguise the message, the author could rearrange the inserted numbers in ascending or descending order (if d = 15 = e, a = 5 = s, and iin = 3 = s, then est = 15-3-5 = diina, but if the letters are arranged in descending order, it becomes daiin).
It's also possible (but it seems strange) that after encrypting the text, the author divided the resulting numbers so that they were the same length, and then added null elements to them. 
Example: we have a set of numbers 3, 4, 89, 01, and 23. We encrypted the text, resulting in 349 89 0123. However, to ensure that each number has an equal number of digits, we split it into 349 890 123. As you can see, the letter 01 was divided into two parts. The simplest thing we can do is this: 349 8901 0223. 02 is not part of our alphabet, so it means nothing and can be ignored. From this series, we can easily get back 349 89 0123 if we know that 8901 is nonsense and 0123 is a word.
However, there are no elements in Voynichese that can be called outright nulls, but there is something similar, namely rows of similar words (choky chol cthol shol, as Torsten Timm called it, "self-citation"). However, this only looks similar on the surface, but maybe the author just divided the words equally without adding any garbage.
In general, the most I can say is that the encryption algorithm is a number-based substitution. And then it's unclear...