Sorry to hear about your situation and a great list of ideas. It's really unfortunate that leaky gut is not well recognized as a medical condition by many traditional doctors. I had some intestinal issues a while back and one thing that was quite beneficial was drinking bone broth regularly. There are some articles saying that gut inflammation can be improved with regular bone broth use:
https://www.bestnutrient.com/best-bone-broth/

At first, I started buying bones and making it at home. It took too long (24+ hours of roasting) so I tried some of the store bone broth brands which ended up being quite delicious and helped improve my symptoms.

Perhaps you are dehydrated? I've upped my water intake dramatically in 2018 and have had much cleaner urine and feel better overall

Cooking bone broth at home is a real pain if you want to do it right. The bones should ideally be roasted for longer than 24 hours and, unless you have a fire pit outside, there really isn't an easy way to do it inside. Also, you want to get high-quality, organic bones which can start adding up from a cost perspective. The good thing is that there are a number of brands that have come to market because of the growing interest in bone broth as a nutritional supplement. As someone who has tried it the old-fashioned way, do yourself a favor and try one of the commercial bone broths out there.

High intake of excessively fermented foods have to be part of this

My nephews gobble that stuff up

IMO, good place to collect your thoughts / meditate or to increase the cycling of water through your body.

Awful.