Stage 1

Bone broths: make soups from beef, lamb or pork bones, whole chickens and save the meat. Best are bones with marrow. Boil them for 2-3 hours. The cartilage on the bones is full of glucosamines and other gelatin substances, which help to heal the gut lining. If fat is not digested, remove fat from cold stock. 

Meat is allowed, but it should be boiled, broiled, grilled or baked. No added fats yet, no frying.
Best way to cook meat is not only in soups, but in casseroles. Buy a nice steak and throw into a casserole with allowed veggies and some self made broth, put on the lid and bake for 1 hour . 

Add only one new food at a time, and add only one fruit per two new veggies. Try new food for 3-4 days, and only then try the next. This is important in case you get a delayed reaction. 

Allowed Vegetables:  spinach, butternut and buttercup pumpkins, summer and acorn squashes and zucchini. Peel and de-seed everything, an cook them soft. If necessary, puree it. 

Fruits: be careful, especially if you have candida or SIBO. Only low amounts, and only cooked and puréed. 

Allowed are: grape juice gelatin (1;1 diluted), pear sauce, apple sauce. If you have problems with fructose, a fruit sugar, try cooked berries before apples.

Mild spices and herbs are legal at this stage.  Use cooked parsley, thyme, oregano, cinnamon and clove (natural antiparasitics), cardamom, cumin, depending on what you like or what you eat. 

Self made yoghurt is allowed, if you are sure that you are not allergic to dairy proteins. Don't try kefir yet, kefir is a really strong probiotic. 

Honey: start with tiny amounts, and be extra careful in case you have SIBO or Candida. Best is raw honey, and even better is medical active Manuka, which is sadly expensive. Eat between one tsp and one tblsp before each meal if you have helicobacter pylori and peptic ulcers. 

If no nut allergy is present, introduce self made pecan nut milk, or almond milk.  Use yoghurt starters for nut milk yoghurt. The lactobacillus acidophilus and the streptococcus thermophilus are very important probiotics. But eat only small amounts.