Unfortunately, you sound pretty typical of a lot of people on this board. There are even a few on here who can relate to their guts getting better while pregnant (although some get worse!).
If you are looking for some suggestions on things to try, here's what I would recommend:
1. Even though you aren't positive for Celiac's on the biopsy, I would go ahead, if I were you, and try a gluten free diet (if you're not already on one). Sometimes you can get false negatives on that test (although the biopsy is supposed to more accurate than the blood test). And sometimes people may not have diagnosable Celiac's disease but still respond to a gluten-free diet. It's worth a try, at any rate.
2. You definitely want to have someone better examine that bile duct problem. Sometimes stones can get lodged in there and are missed when they remove the gall bladder. Sometimes there is just damage to the bile duct, either by natural deformity or by surgical accident. But either way you can continue to have pain like from a gall bladder attack from a messed up bile duct and they need to fix it or, if possible, remove it.
3. If you suffer from diarrhea, there are two things you can try for relief. The first is Caltrate 600 w/vitamin D. It's a basic, over the counter calcium supplement (has to be that specific brand/type or it's generic equivalent to work, though). You can take two a day. Calcium does two things--one, it absorbs water in the intestinal tract, thus helping diarrhea problems and two, there is some evidence that calcium helps soothe irritated intestinal linings (perhaps the stomach as well) and that may help with pain and diarrhea as well. The second thing I recommend you try, since you have had your gall bladder removed, is a prescription medicine called Welchol. It is a cholesterol medicine, but they have found that it (and a couple of other cholesterol meds in the same family) work very well for people who have excess bile in their intestines; it soaks it up. My G.I. put me on it a couple of years ago now and I have benefited from it greatly. I take one pill every morning as a preventative and then take additional pills if necessary to stop diarrhea.
You are right in suspecting genes; most all of us on here have at least one family member with gut problems. My mother's had her gall bladder out and has GERD, two of her relations have Crohn's, and my Dad's had a ruptured appendix. Actually, if you start talking about gall bladder problems in my family, people start coming out of the woodwork.
Unfortunately, there's nothing you can do to undo your son's genes. IBS is not preventable. IBDs are not preventable. If IBDs run in your family (Crohn's, Ulcerative Colitis), then you will want him checked quickly if he ever shows any of the symptoms, because I have heard that early treatment keeps it from getting as bad. But unfortunately there is no preventing any of it, nor making any of it go away.
I think the best thing you can do for your son is to put him on a really healthy diet at a young age. They have found, for instance, that gall bladder disease seems to be more prevalent in Southern people and that has been blamed on our tendency to eat everything fried. However, there is no concrete evidence that this is the cause; a lot of Southern people have Scots-Irish and Native American roots and I happen to know that Native Americans are more prone to gall bladder disease than just any other race. I want to say that the Scots-Irish also have a problem with it. But, in any case, fatty foods seem to make gall bladder attacks worse, so if you get your son used to a diet low in bad fats, even if he is destined to have gall bladder disease, his diet may delay it or make it not as bad. It also makes it easier to adapt afterwards to not eating those things that make you have diarrhea--fried chicken, for instance. Also, if you go on a gluten-free diet, put him on it as well. Celiac's disease is herditary and a link posted on here a couple of days ago on Celiac's disease said that there is some evidence that links gluten intolerance and IBDs, and that when Celiac's disease is caught early, the chance of developing an IBD and other auto-immune disease later goes down by a good deal (Celiac's disease does not cause auto-immune disease that anyone is aware of--it itself is one, I believe--but the constant irritation caused by a reaction to gluten can spur the body to develop other types of auto-immune problems).