it may be the fiber that is giving you trouble. So give your body as much help as it can get....make puree's...things that are filled with veggies, but they are already quite broken down, pea soup, fruit smoothies, etc.

I'd just experiment with certain ways of preparing and certain foods. One day go crazy with creamed corn, another day eat lots of chicken, etc...and just see what your body is willing to process. At least it will give you options for fueling your body until you get the health stuff figured out.