When you complete the detox, you should have a list of foods you eliminated and then added back in. For 8 hours after you eat a food you’ve added in Phase II or III, note any gastric disturbances (bloating, gas, discomfort, constipation, diarrhea) or other symptoms, like headache, fatigue, skin reactions, etc.
Some foods that are very good for you can cause a reaction. For instance, my experience working with thousands of people on whole-foods habits is that highly detoxifying foods—especially greens, vegetables, coconut oil, homemade granola, etc.—will cause people’s digestion to change, sometimes radically.
The obvious conclusion, for people who have not studied nutrition and for whom nutrition has not been a priority, is that this is a food that does not agree with them. It would be premature to make that conclusion.
If all green foods cause detox reactions, it would be a tragedy to eliminate the most important class of foods there is. It is, then, worth it to complete an extensive cleansing process and see if digestive disturbance caused by those foods calm down.
Grains causing sensitivities are another matter. You can eliminate them without causing significant deficits in your nutrition, since grains are nutritious but their properties are found in other foods. Probably due in part to genetically modified grains, most people have anywhere from a mild to a severe degenerative gut issue.
Unfortunately I cannot give you a definitive chart of answers related to specific foods and their reactions. People are highly individual. This will require the analysis of a naturopathic doctor, or another physician trained in diet/nutrition, food sensitivities, and holistic health. However, the food sensitivities chart in Appendix A is a good starting place for you to explore what foods to eat more or less of.