Is that the only reason my body has a hard time with whole food?

   According to the enzyme bank theory, we only have a certain number of enzymes inour body from the time we are born until we die. When you eat cooked, processed foods, your body comes to your rescue by providing enzymes to digest it. As you get older, you may not have the enzymes necessary to digest your food properly because you have used them up digesting cooked processed food.

   There are other reasons you may continue to have problems even though you are trying very hard to make positive changes in your health. Your digestive system  may be compromised after years of eating a Standard American Diet (SAD). Your intestinal tract maybe coated from old undigested foods, preventing good nutrition from getting into your blood stream. Your organs may be slowing down in their ability to process foods. This prevents good health due to clogged plumbing in your digestive tract from a back up of undigested foods that never left your body. You may have lost organs due to surgery. Poisons and toxic substances that are stored in body fat and in joints for years can cause aches and pain.
   As you go up the food chain, there is an increase in the toxic load on your body. Plants may have small amounts of pesticide residue on them - but these are water soluble so you can wash that off. A small amount of toxins make it into the plants, but a healthy body can usually eliminate those. Animals eat plants - tons and tons of plants. Their bodies then concentrate these toxins. For example,in the oceans, tiny animals eat plankton, getting tiny amounts of toxins like mercury. No big deal yet. But bigger fish eat smaller fish, concentrating the mercury at higher levels in their bodies. When you go all the way up the food chain to tuna, you get the highest concentrations of mercury.