I've also heard that they took out a part where you can see the track briefly that the boulder rolls down. I personally haven't looked for it, but I think its something you have to really be looking hard and slow the film down to see it. Nothing that was that big of a deal.
As for the documentaries, I don't know why they didn't include them. But thanks to some people on this board, they are available. I've always thought that the classic documentaries were better than the new documentary in the DVD set.