It sounds quite clear that you have post-infectious irritable bowel.
You have had an extensive work up for ongoing infection and other causes and they seem to be negative. It is not uncommon to develop an "irritable bowel syndrome" after an acute infection- the symptoms as you describe, with bloating/ indigestion etc...
The couple things that you did not comment on is if you were tested for Giardia ( a different parasite) and for helicobacter pylori ( a common bacteria that can cause many similar GI symptoms.
If those two tests are negative as well, I would suggest "supportive care"- this may include increasing fiber in your diet, avoiding foods that do worsen symptoms- like lactose products, but also greasy or fatty foods, and taking antispasmodic or antacid medications as needed.
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Anti-spasmotics are medications that work on bowel spasm- like Bentyl.
I would not, however, advise you take that in pregnancy.
I would try to increase fiber and see if that improves symptoms.
After pregnancy, there are several treatments for irritable bowel that you may want to ask your doctor to try, including rifaximin, tricyclic antidepressants, Amitiza, or antispasmodics like I mentioned before ( Bentyl, Levsin). I would not use any of those in pregnancy however.
I do think you can be pretty confident you do not have "an organic" cause and this is an irritable bowel.