Hey Sean!
I am using short note length because this is the type of sound I want, I just amplify it for the tune later on.
The 64 voice limit helped partially, but it seems that this is what I fixed when went for two separate WhySynths.
It is now much better, however from time to time, once in 10-15 seconds, there is still an audible click.
This seems like less of an issue, since when I was using two WhySynths, it seems that both were generating these clicks,
thus making them sound more often. Right now this is barely noticeable, but still there. Try to listen to the progression for some time
and you should spot them.
But your suggestion still helped and if nothing else helps, I might use this version.
Cheers!
L.V.