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It's a process for sure. Interestingly I was living overseas for a few years, (eating real food because they have real food) and I felt great. My husband who always suffered from indigestion and all the classic middle aged male stuff wasn't having any of it. He lost 20 pounds in the first three months.

(BTW, we're doing ok, thanks).

Restoring gut flora fixed my IBS. Yogurt, that's it.

I later figured out my gut flora (the good, the bad and the ugly) had been wiped out by a simple dose of antibiotics.

Food for thought... IMHO:

Basic stuff that works fantastically well if done on a daily or almost daily basis:

Increase animal fats (bacon and eggs is the bfast of champions)
Real butter, real eggs, real dairy (raw, unpasteurized unhomogenized if you can get it, never low fat)
Oatmeal your only cereal - every day or almost
Whole milk yogurt every day or almost
Decrease carb intake
Don't eat so many carbs
Don't stuff your face with cakes, pasta, bread, cookies, rice, potatoes, noodles
For a real treat, fry your own potato chips, apply sea salt and have just a few dipped in real whole sour cream
When bread, only bread made of: flour salt water yeast
Bake your own cakes/cookies/crackers/snacks (avoid bad stuff by eating none of these that are manufactured)
Lots of varied veggies cooked interesting ways
Use quality (or make own) stocks: beef/chicken/veg
Learn and use herbs and spices to put flavor in food
Increase house/yard work/walks/jogs, on an "irregular" schedule
Heavy exercise occasionally
Drink water - big glass at meals & in between
If you "need" something else, ice tea made from tea bags (nothing but tea) or lemon water

If ingredients say "natural ingredients", that is allowed to (and typically does) include MSG which is bad.

Try to avoid medicine, even aspirin. Try coffee, beer, wine, whisky, etc., instead. Research every medicine before you take it; reject what does not pass muster.

Gut flora out of wack knocks leads to immune system dysfunction.

Inflammation is natural of immune system, but it's rampant out of control all over from diets and medicines.

Not getting enough animal fats is a slow long-term killer, causing all sorts of chain-reaction problems.

Too many carbs is same, long-term killer.

Many on FR probably have found similar things, so of course this is not anything really "new".

I am doing many of the things on your list. I was never a bad eater but I did quite a bit of things that I coulda done better.

I had one diet soda a day, I cut that out and do the sun brewed unsweetened tea. I live in Phoenix, I can sun brew a gallon of tea in an hour. LOL.

I got rid of the fake healthy bread that I *knew* was crap but chose to believe it was better. I started buying unsprouted breads.

At night, I take about an ounce of Braggs apple cider vinegar with a huge glass of water about an hour before dinner.

Switched to organic or at least non-BST dairy. I cut milk out altogether as it wasn't agreeing with me and switched to almond milk. Just look at the ingredients on all the mainstream ice creams--just a chemical cocktail.

I make a green smoothie every morning. I had been doing that only sporadically.

I already have been a runner since I was about 15 so I know there are two things I need in my life to stay (reasonably) sane. 1. exercise and 2.sunshine.

Oh, and I drink one large glass of water with chia seeds every day as well.

No doubt the gut flora is key. That is what is concerning about some of these GMO studies.

Once you start educating yourself about what exactly some of these chemicals are eating it becomes a lot less tempting. Not really thrilled when seeing BHT listed on the label anymore.