Atoms and elements of the Voynichese alphabet

[Stefan Wirtz_2]

I do have observations that led me to believe in the frequent mis-reading of in as r, and of d as k or vice-versa. But I suppose you would dismiss them as mere coincidences...

There is no valid way to make a difference between conincidence and correlation within observations about VMS details; so yes, it is a portion of believe to step up to correlations — I would not follow there.

The rate of errors can be very high.  The diary of the Lewis and Clark expedition is full of mis-spellings;
[..]
And yet the authors were US Army officers who went through a military academy, and of course knew the language...

That is a nice anecdote, but not very much surprising: most major languages, even western ones, did not get a universal standardization of grammar, spelling etc. until the end of 19th century. 
Of course, all earlier scripts could have been or were indeed written quite wildly in all regards, even by one and the same scribe.
Your example is set to insinuate that some foreigner may have made a lot of spelling errors with (for him) strange vocabulary. It may be or be not so — but there is no sure hint that VMS was made by „foreigners“ or native speakers just writing in a (for us) foreign alphabet.

At all, this here is still dedicated to gain a roster of observable, smallest autonomous or atomistic pieces of this character set — you added some interpretions to your point of view onto that alphabet, but this cannot be quite comptible with my initial idea. 
Looks like I have to upload my own transcription some day.