I only had a chance to scan through the main page and go back and read about 50% of it but it looks quite good to me. The only thing I am trying to figure out is whether the Mod Warp and Mod Glide parameters would make more sense after the reader read the description of the mod matrix rather than before. In that case, there is of course the issue of continuity, since it all goes from top to bottom, left to right up to that point.
I suppose one solution would be to simply mention to the reader at the start of the Mod Glide and Mod Warp sections that that they might want to read about the modulation matrix before reading the rest of the section.
But really, I’m nitpicking: nice manual with clear screenshots and a good outline of the features. 🙂