What tools do you use for VMS analysis?

[asteckley]

I just recently started using mysql, but find it cumbersome, and what I though should be easy: fill a database with ready made CSV files, so far has been prohibitively complicated.

I too started using MySQL to maintain and manage the VMS transliteration data for analysis purposes, but very soon discarded the idea. 
You are correct that, for this purpose, it (or any SQL database for that matter) is just cumbersome and unnecessary.   In data processing terms, the VMS is.. well, tiny.  The extra overhead of dealing with a persistent database just isn't warranted, since the entire manuscript and all its components can be easily held several times over in RAM on a laptop.
So reading in directly from an IVTT transliteration file and/or from CSV files is more than sufficient.

I do, however, use MySQL behind applications like The Voynich Garden and also for clipping and managing graphical elements from the Voynich hi-res images.
This was mainly necessary because the graphical editing work is so meticulous and time-consuming, that it is worth persisting each action to disk so that I can backtrack editing mistakes and not lose my work when I accidentally fat-thumb a deletion.

On a separate topic though, and pardon my rant: 
I must disagree with the "terrible reputation" claims on MySQL.  I've used it for several large-scale commercial and mission-critical implementations with great success. Any failures concerning security or reliability would result from its hosting and implementation infrastructure, and any other alternative database (e.g. Oracle) is equally vulnerable to that. The criticisms of it almost always come from those with a vested interest in its commercial competitors.  I abandoned Oracle a long time ago, after spending almost 2 years listening to Oracle's account reps trying to explain and justify their outrageous calculations on how they were billing us for it. And subsequently confirmed that it just offered no significant features or advantages over open-source databases like MySQL or PostgreSQL.