An explanation of the Voynich Manuscript text

[Torsten]

You can't apply propositional logic.   There's a huge amount of modality, probability, and fuzziness involved here.   Things can be possibly true, probably true, or quite true.

Clustering is very much a black art.    There are no clear breaks between contiguous clusters, and their differences are small, e.g. for blue and black herbal.   I could have drawn the clusters differently, e.g. subdivided them or moved their boundaries slightly.  Also, if there's randomness, you're going to get some overlap.   What it might help elucidate, is the order in which the text was written.

There are places in the text where word frequencies do change abruptly between non-contiguous clusters, e.g. f26r, from green to red.

Similar words co-occur because they're frequent within certain pages clusters, e.g. the red herbal (Currier B) pages have a high frequency of words ending in edy.

This is exactly my point. The parameters used for clustering are subjective. Other clusterings are also possible. There are notable differences between two clusters. This means another interesting clustering would be to use a cluster for each quire or for each page of the VM. This way you would get smaller differences for two contiguous clusters.  If I understand you right you use one state transition table to simulate each cluster. This means as more transition tables you use as more detailed is your simulation.

This would be no problem if you would argue that you use transition tables to simulate your results for the VMS. But since you claim that the text of the VMS was generated using your transition tables I see two problems. 

The first problem is that you explain the differences within a cluster away as random. This is problematic since the details you see only depend on the number of clusters you use.

The second problem is that you use different transition tables for each cluster segment. As far as I see you didn't give an explanation for the changes between two transition tables.  One explanation I see is that for the VMS a unknown text generation method was used and that the output for this unknown method changes over time. But this would mean that your state transition tables are only a way to simulate some of the output of this unknown text generation method. This would mean that your state transition tables can be very useful to learn something about this text generation method. But this would mean that they are only a simulation not the unknown method itself.