I actually DO have a FDS that I got in a ''Junk'' lot from Yahoo Japan for peanuts. Quite a long time ago. It was never able to read disks but it might do for playing music? Can the extra FDS channel be accessed with a flashcart ? The extra FDS channel kind of scares me though, hahaha.
Also, I remember from years ago when I was pretty deep into console repair and modding, some folks were selling ''blank'' boards with expansion audio chips. They were intended for making repros. You just had to burn the ROM and install it in the board. I have a Gimmick NES repro that as far as I know was made with these. I meant to modify my NES to be able to play expansion audio but I never got around to it. My days of modding were a bit cut short when I became an ebay powerseller and my focus shifted.
The one thing that bugs me is why are the waveforms not aligned the same at each playthrough? If the reset points are predictable, does that mean that there is some randomness to the initial state of the waveform when the generator resets ? Or do the channels drift from each others over time ? Your explanation on what triggers the reset is indeed somewhat lost to me but what I do get is that it can be triggered by the right sequence of events. Maybe this can be exploited by playing some short ghost notes, will the reset still occur if the volume of the note is 0 ?
Using the pitch enveloppe to further control these issues sound like a good idea. Somehow I had not realized it allowed for such fine adjustments. How is ''one pitch unit'' defined ?
By the way I replied to your question on youtube in case you did not get a notification or something.