I don't know that the stoma would require anything special.
Peat's ideas for reducing serotonin/endotoxin, which I think would apply to equally to the stoma, might be broadly summarized as:
1) Avoid bulk in the form of fiber or starch,
2) Use the quinones to maintain good motility and reduce inflammation, and
3) Improve the gut and liver by boosting oxidative metabolism; there are any number of creative, fun ways to do this with diet and lifestyle.
One thing you might want to try is irrigation through the stoma with hypertonic (5%) saline and urea (not plain water).