The real answer to this is to pay attention. The body has all kinds of warning signs and notifications, but most people don't pay attention to them.

For example, after you finish a meal, do you feel like you ate too much? You probably did, and yet most people have it so ingrained into them by their parents to finish everything on their plate that they overeat, which messes up your body's metabolism (it thinks there's a glut of resources and converts to 'store fat for later' mode).

A past roommate used to have a huge problem with his skin, lots of acne and rashes and so on, until one day he had the flu so bad he couldn't get out of bed for a few days. His friends were literally bringing food to him at his apartment because he couldn't get off his couch. By the end of the week, his skin had cleared up. Within two days after recovering, his skin had gone to hell again. Sick again, healthy skin.

After analyzing it, he determined that the only significant change (other than actually being sick) was his diet. He made a list of all the things he typically ate, and introduced them back one by one. Turns out eggs, which are 'good for you', were an allergen. He cut them out of his diet and he's been healthier, sick less often, clear skin, and a host of other minor improvements.

If you eat something then your stomach feels upset, stop eating it. Get a little note pad and jot down what you eat whenever you eat it, or just make a note in your head. If you start feeling unwell (stomach, headache, etc.) 20-40 minutes later, make a note of what it was, and cut it out of your diet.

One day, just out of high school, I was cleaning up my desk at home and realized that most of the pop cans I had on my desk were half-full. I wasn't finishing my Dr. Pepper, even though I really liked it. Then I thought about it and realized I didn't really like it. I used to, but I kept drinking it out of habit. Still, if I wasn't finishing it, I must not like it that much. I stopped buying it. I've since cut out all canned beverages and fountain drinks. After a year or so, I discovered that I can no longer tolerate them. I've removed them from my diet, and now my body doesn't have the resistance it's built up to them.

I could probably build up a tolerance to them again if I wanted, but why would I do that? You shouldn't be eating or drinking anything you have to build up a tolerance to.

For your specific case, make some notes of how you feel, and then change things. Take a baseline, then add more protein. Take some Omega-3 supplements, remove carbs for a week or two, and see how it affects you. A step-aunt's autistic son went from unmanagable to a sweetheart by removing processed carbohydrates from his diet. No toast in the morning, no pasta in the evening, and suddenly his mother's living hell became a relative paradise.

When in doubt, remove all the artificial, pre-processed crap foods from your diet. Shop, as one poster suggested, on the outside walls of the grocery store – meat, fish, poultry, vegetables. Try taking dairy out of your diet. Try taking sausages. I can't digest animal fats, so both of these are bad ideas for me. Same with bacon. Try taking things out. Reconsider everything in your diet, and don't be afraid to play around. Add things, remove things. Read other people's experiences. Make notes, and learn from them. Build hypotheses and test them. Approach it like a science experiment, because that's really what it is.