Ditched the (literally) hacked PCB for MIDI I/O and instead been using Hairless MIDI<->Serial Bridge:
This allows me to not have to use a physical switch to make my uploads possible, but instead I just click on a checkbox in Hairless to do that.
On Mac OS X, it is a bit flaky when you click to re-enable the Hairless bridge. It sometimes won't be able to re-create the objects used for communication. The solution is to exit and restart Hairless each time. Works for me although a slight annoyance.
And so we've got 115000 or above Serial() communications between the Mac and the Arduino. This also means that I'm not limited to MIDI-2-CV with the Arduino to the Polysix. I could use another piece of software and send that to the USB port if I'm not mistaken.
Additionally, I rewrote everything to use the MIDI library v4.0, re-structured the code to use callbacks and the 16-bit timer in a faster than usual PWM mode, so that MIDI reads are faster/tighter.
Moreover, I decreased the timing of pulses down to nano-second levels with a faster digital write.
Very pleased with the results I had yesterday after testing with the Polysix Arp driven by the Arduino and sync'ed to the MIDI clock of the Kurzweil. Super tight timing, great bass Polysix Arp, JX-8P pad with Kurzweil K2500XS drums, very musical, very electro/80's, and definitely basis for composing new music. Expect a Soundcloud link too soon.
Yash