I apologise in advance, I haven't read the entire thread.
Now, I have read the class description on the front page, and I can tell you one thing immediately: Some of the bonus feat progressions are off. You'd want many things earlier, and others later. Of course it might be thematicaly wrong, but it's still supposed to be a D&D class, right?
Things like this:
Infantry Archer: You are one of the lower ranking Samurai, standing in the back with masses of longbow archers. You gain the following Feats: 1: Point Blank Shot, 4: Far Shot, 7: Precise Shot, 10: Improved Critical (Composite Longbow), 13: Sharp-Shooting, 16: Penetrating Shot, and 19: Improved Precise Shot.
Precise shot, for instance, is just way too late. Unless you wanted to give the person an open bonus feat of course (at best state clearly that if you already have a feat from the bonus feats, pick a free one). Now I know that you are envisioning an infantry archer who stands around in a group of archers shooting at enemy formations, but what's the point of making a D&D class option if noone is ever going to take it? Noone is ever going to play a samurai in such a hierarchy. And NPCs don't need that much attention to detail.