Love it, William.
I've no knowledge of late Renaissance/early baroque music but it seems to me you've brought this darling piece very much to life. I easily imagined people happily twirling and hopping around the dance floor to this piece back in the day.
I assume you changed the root key to G in the VIPro tuner, because it all seems to hang together quite nicely - even though the serpent player does indeed sound like he's almost off his trolly, LOL.
I ran the piece through Melodyne Studio. Celemony don't claim to be able to analyse polyphonic ensemble pieces, nevertheless the Melodyne analysis generally showed a reasonable match to JI in G major.
One of JI's worst flaws is that the minor triad on the 2nd degree is broken and has to be avoided like the plague. This triad has a "defective fifth" (it's a comma short of the pure perfect fifth) which is grotesque and unusable, and the third is Pythagorean. In this piece Pretorius appears to have avoided using the A minor triad, and I guess composers in his day would all have known not to use a minor triad on the supertonic.
Anyway, it's a really nice, very smart and very enjoyable step back to the simplicity of the early 17th century. Bravo, William.