The Book Switch Theory

[ReneZ]

why the Jesuits decided to sell books to Wilfrid

This is well recorded in the letters that were found in the Vatican, but already clear from a paper written by F.Ehrle. They got significantly more money from private booksellers than from institutions. At the same time it was unsafe
to sell all to him.

why he kept Marci's letter hidden for years

I agree that it is hard to understand why he was not interested in it. I don't think that he was actually hiding it.
He referred to its contents (incorrectly) in 1915.
He was only interested in the Bacon origin, and had simply not understood the letter at all. He thought that the Rudolf mentioned in it was Rudolf I, a contemprary of Bacon. He had no idea at all who was Marci.
I guess that his Latin may not have been good enough. 
It's only when Newbold was indicating that he could read the text, that Voynich decided to investigate the later history of the MS.

why the VMS is not clearly described in the records of the sale, ...

Any records of the sale (presumably in the correspondence with Strickland) were destroyed by Voynich.  
Some of the remaining items have pencilled comments saying: "do not destroy" and "safe to keep"
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Why wasn't  Marci's letter included in the Carteggio?

We don't know exactly why, but Fletcher, who studied the Carteggio over years, clearly states that this collection is incomplete, among others from cross-references. Perhaps the organised filing only started later? Just guessing.

Edit: by the way, the other manuscripts were valuable above average. A summary of prices is a recent addition here:
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