I've been looking at this piece today using the facsimile available from IMSLP. It's worth noting, perhaps, that Libro primo d'intavolatura di lauto is a printed book rather than a manuscript - however I don't think that guarantees it is free of errors!
You chose to notate the piece in A minor. I had a look at your transcription and noticed that using MuseScore to convert the tablature to notation puts in in G minor. However Luthval's performance (presumably on a G lute) sounds in F minor, a minor third above D minor which is the key it sounds in if you read the tablature directly on the guitar.
Taking my lead from this I transcribed the piece into D minor, discovering that you can play the whole piece as notated apart from 4 low Ds, one low C and 4 low As (all but one of which are also in the tablature an octave above). Available on my website and in the scores section of this forum.