I agree with shroom about the items showing up in the stool. When the gut is damaged then you get undigested foods. shroom brings up a good point about enzymes which are necessary for the breakdown of food. You have 2 sets of digestive enzyme functions, the first is the stomach which involves HCl and pepsin, I believe both of these are directed towards the digestion of animal products.
The second system involves the pancreas which secretes a number of different enzymes such as lactase (enzyme that digests diary), lipase (digests fats) and a whole bunch more. There are supplemental enzymes you can buy.
However if the gut is harboring infection then this will irritate the gut which results in IBS. You can try to harmonize the gut with things that help the healthy bacteria proliferate such as vegetables, fermented foods and some kefir. Colostrum aids in this as well. I am a big fan of turmeric which will aid the gut, inflammation, regulate stress responses and on and on, research this wonderful spice.
The above would be an effective treatment for most bacteria, some yeast/fungus and possibly viral issues.
If this does not solve the problem then you look for other pathogens such as parasites. Many overlook the protozoa species, these are quite harsh bugs. Testing is very hit or miss which makes the equation more difficult.
After 25,000 hours of study, I can make the conclusion that the body is a very interactive system meaning that defects in one area will affect others.