Welcome to curezone. Everyone is very helpful here.
Well, I am not familiar with that book, but did you use something to soften the stones like phosfood liquid, apple juice, or malic acid for a few days pre-Flush? I think the indigestion could be a result of the toxins still remaining inside the colon. Did you go for Hydrotherapy (Coloniccs with water) or do a series of enemas after? You have to, or else the toxins will be reabsorbed, go back to the liver, decrease the liver function of an already weakened liver, thus causing low bile and digestion will be incomplete without enough bile. Also, you diet should remain fat free or low fat, basically vegetarian for a few days after the flush. The first day should be all fresh juices. This is because the Liver Flush is like a surgery to the liver, the liver needs time to heal. It can't go back to work in full force.
Don't worry, we have all made these mistakes. It takes practice. Some other people may respond with even better advice and tips. You will definitely do much better during your next flush. (Wait atleast two weeks between flushes). I strongly reccommend the "The Amazing Liver Cleanse" by Andreas Moritz . He has a forum here and answers a lot of questions. Also click on "Clark" above and you can read all about her protocols and liver flush. Also Dr. Kelley DDS, who discusses curing cancer, talks about Liver Flushing and Metabolic Typing. Metabolic typing tells you which foods are good for your metabolism. Although, be careful the new version by Wipincott is stolen from Dr. Kelley and done over completely wrong.
There is a lot of good info on curezone. Keep searching, you'll find all your answers.