I used to do very well on low carb diet many years ago.
The past few years it is getting worse and worse in some respects...
When I stick to mainly meat, fat and veggies I have almost perfect digestion, but i gain weight like crazy, feel too hot, irritable, symptoms associated with liver heat/congestion. The meat/veggie diet also detoxes my small intestine very effectively. But the problem seems like it has gone on for too long, whereas most people seem to detox in months or 1-2 years mine has lasted forever.
What type of meats are you eating? Is it organic/pastured/free-range/wild-caught?
On the other side of the coin, if I eat mainly carbs, even healthy ones, my digestions is terrible, loose unformed stool. But, my mental state is much better, happier, peaceful, more energy, and my weight is very good.
Carbs turn to glucose quickly in digestion, it's a good feeling in general. Meats and veggies don't offer the quick burning sugar your body craves, like an addiction. A little bit of carbs is good for digestion, you don't need to have only carbs in a meal.
I'm also getting the sensation that a lot of vegetarians complain of when they eat meat as if they are getting the feeling of the adrenaline when the animal is killed. Or it feels like your body is being poisoned when eating meat. I hadn't felt this while eating meat for 15 years but it started to become more and more apparent recently.
Much meat is processed with antibiotics, growth hormones, and specialty feeds, especially farmed meat. Even wild caught, they layer preservatives on the cuts.
What could cause the disparity between digestion and the other body functions, it would make more sense that when digestion is good then the other functions would naturally be better as well?
Unfortunately, many foods are dead on arrival to the plate. The biodiverse flora is gone or few.
If I were you, I'd get a blood screening for food allergies and get a profile of foods that you might be allergic to. Before the test, eat all types of foods for a few weeks to expose your body's innate immune system to the potential sensitivities.