Well reading from the first page, he says that with the Auto Simplify Curve option enabled it will change the shape of the spine a little. And you can lessen the effect on the oriented joints by simplifying the curve of the joint chain (straightening).....

read part 1 again so this is clear first of all. With rigging it does take a bit of a mindset to get round what is going on and why things do what they do. I'll have a look thru this stuff and see if I get any probs and get back to you later. It should be pretty straight forward but as you are doing a rig thats for back stretch there maybe an easier way

Jay