Why doth the body protest a healthy diet so much?

Sounds like to much too soon. I hope you will start to feel easier. This is highly controversial on here but living in the UK where we are blessed with some really good, I mean, interesting health related programmes on all our principal free to air channels we are hearing more about digestive microbes. Consuming a diet of highly processed foods along with a diminished range of vegetable variants because our food producers have settled on main strains and also our use of antibiotics and other medication have all reduced the number of microbial species our bodies contain which do everything from breaking down foods to creating enzymes and facilitating the uptake of vitamins and more.

It is possible you are over doing the fibre, the amount mfp sets is good. Some scientists say we need even more. But in the short term until your body gets used to this new regime the fibre is helping your microbes replenish themselves but also it is clearing out the system. I would say, hang on in there, you will get through it. Make sure you drink plenty of water and during this very hot period do not forget the salt.

I remember when I started eating beans. (The stories, they are true.) I now eat 2-4 kinds of beans every day and my stomach is chill with it. It took about two weeks (building up slowly, getting my body used to one new food at a time) for the gastrointestinal upsets to stop. I also took probiotics and digestive enzymes during this time as a crutch to help me out; you might look into those (they're cheap, and you don't have to take them forever).

Benefits of a healthy diet that I've observed:
-Better/faster muscle recovery (key with me; I bike 5 miles a day and walk 5 more and go to karate practice and...you get the idea)
-More fun/self-sufficiency in cooking (I never learned to cook as a kid and boy howdy am I making up for it now), plus more meal options, plus the satisfaction of choosing exactly what you want to eat
-Depending on how you do it, it's cheaper. (Spinach, broccoli, carrots, apples, honey and berries are quite cheap, fresh or frozen, where I'm from. YMMV, but if you focus on getting food that's in season, you can spend less than half what you did on the pre-made/processed stuff)
-Skin looks healthy and glowy and pinkish. People ask me about it. It's weird.
-I'm never sick anymore. (Last time was...January, I think? And that lasted less than two days...)
-Fewer cravings for the junk (not saying they don't happen; I'm saying that satiating food makes you less hungry overall)

My advice is to pick one change at a time, stick with it, and add another. System shocks/upsets aren't necessary to achieve a healthy diet.