Fixing your digestion should be one of the top priorities along with cleansing. If you have undigested food in the bowels it means they weren't properly broken down (obviously). And in order to properly breakdown food you need several components, including proper chewing, saliva, stomach acid, bile, digestive enzymes. Also importantly, is the food combination and order of things. Rather then going into detail, here's a site that best describes digestion: http://tuberose.com/Digestion.html
Curiously enough Liver Flushes may be one of the best things you can do to improve your digestion as it removes stones that are blockng bile flow (bile is critical for fats absorption and pH balancing). If you eat cooked food mostly you want to make sure you supplement with digestive enzymes since your body may not be able to keep up with your cooked food intake (uncooked food has enzymes). A lot of people who complain of excess acid actually have low stomach acid.
You may also want to look at healing your gut - undigested food particles should not be seeping into your blood stream (leaky gut).