Hi Vcast,
I rebuilt my digestive system before I started Lyme treatment, so I have some experience - don't know though if it will serve you - but this is my bit... maybe you can use bits of it...
Try to determine if you have any food allergies or intolerances (US Biotek Laboratories is a good lab, I'm in no way connected to this lab, just my experience - I sent my blood from Europe to this US lab), look for a good nutricionist, who will help you with intolerances, diets and ideas for food. Don't eat any sugar, as less processed food as possible, no artificial sweeteners, no additives if possible. Food allergies/intolerances are highly underestimated, they can cause serious problems.
I did a faecal test, to determine what bacterial overgrowth I had, which ones I was lacking of.
For my stomach: did a gastroscopy to determine if I had gastritis or something else going on - got medication (nexiam - 28 days) for that.
After that: good very strong probiotics (I used Mutaflor, but I'm from Europe, it's made in Germany I think). I did the probiotics - antibiotics procedure (some drs think it's crazy, but it just cured my gut): kill gut bacteria with abx (enteric coated), replace by good very strong probiotics, kill again, replace again - etc etc for about a year, until I was cured. Also took a medicin against bowel inflammation, just 2 months.
What a difference: no more cramps, no more diarrhea, no more nausea, no reflux, everything was cured (until I started Lyme treatment, everything down the drain - but I'll rebuild it again once I'm better, I'm trained now - lol).
Hope you got something out of this
Good luck!
Marie