A great way to get a behind-the-scenes glimpse of these videos (and Bill's production process in general) has been to check in on his vimeo accounts ([1] and [2]).
It's not quite what you're looking for (a simulation of the machine, which would be amazing to see in its own right), but according to this video [3], it looks like they've built a neat webapp for the purpose of having a sort of fourier synthesis playground.
Unfortunately, there's just the demo video, with no link to the site itself, and searching turned up nothing. They may plan to release it later on in the series.
[1] http://vimeo.com/engineerguy/videos