If you read the book you'll understand. The Intro kills off all the bad bacteria. Slowly adding in new foods will enable you to figure out which ones bother you and which don't. Sometimes a food will bother you in the beginning but later you can eat it as the good bacteria are built up and your gut heals. I say heals, but if you went back to the SAD you'd probably develop problems again so remission might be a better word.
You could always just try jumping in. It works for some people. I'm in remission on Imuran and just jumped in. However, I am having some cramping and fatigue and a lot of gas so I'm going to be forced to go back to the beginning and go slower.