Regarding secondary health issues etc, a ND once used an analogy which I like. He said you must fix the problem most 'upstream', because everything 'downstream' is ultimately affected by it. Using your analogy of the leaky boat, it's not much good plugging holes if you don't also plug the madman with the hatchet!
Priority #1 is to identify the pathogen X, and/or, find something that kills your pathogen X (where pathogen X is the microbe responsible for causing your leaky bowel). I think for most of us with leaky gut, pathogen X is fungus X, but not always. Likewise, fungus X is usually Candida albicans, but not always.
Until you fix the problem most upstream, and for most of us this is Candida, it is almost futile trying to fix downstream problems like leaky bowel, allergies, adrenals, CFS, depression, anxiety etc etc.