Gawz, I'll try to address your questions as best I can. Not a doctor yet, but I am very experienced with gut issues, especially diarrhea, so I'll try to be as helpful as possible!
If you have a normal TSH, chances are your free T3 and T4 levels are normal too. Someone with an overactive thyroid (hyperthyroidism) will tend to be more prone to diarrhea or more frequent bowel movements, weight loss, excitability, "hot flash"-type symptoms, rapid heart beat, and excessive fatigue. Usually the labs will indicate a low TSH and and elevated T4 in this case. Someone with an underactive thyroid (hypothyroidism) will exhibit constipation, weight gain, lethargy, and feeling cold; in this case the labs will show elevated TSH, but in some cases not.
The diagnosis of thyroid disorders is usually straightforward but can take time. If you think you have a thyroid issue, a full thyroid panel wouldn't be a crazy idea.
Nausea, abdominal pain, urgency, and frequent BMs or diarrhea can all be hallmark symptoms of IBS and this is the diagnosis usually given in the absence of physiological findings on tests such as the ones you've had. Obviously, it can be a very debilitating condition, and it can take a long time to optimize the treatment. The fact that Bentyl helped you for three years is a good sign; there are other antispasmodic drugs out there, like hyoscyamine, that can be tried if dicyclomine is no longer working. Or you might want to simply try the dicyclomine again. You shouldn't take those anti-spasmodics, though, unless you're really having pain. You don't want to take ANY prn (as needed) medication every day unless you are really having pain every day! Your body builds up a tolerance to drugs very easily and you have to be very careful with them.
This is what you really have to do: seriously eliminate all products containing yeast for at least two weeks. That includes beer, any other liquor with yeast in it (I have no idea which ones do), everything! It may be difficult, but it's really the only way to tell if that's truly your problem.
If that doesn't eliminate the problem, you can consider the following:
The tests you haven't had done yet are the small bowel series, lactose breath test, capsule endoscopy (anyone ever brought this up to you as a possibility?), CT scan, and abdominal ultrasound. Also, check over the stool tests you've had and see if they did these: ova and parasites (at least three separate O&P tests), fecal occult blood, and fecal leukocytes. These stool tests all should have been done way back in the beginning. The small bowel series, like I said before, can check for areas of narrowing (strictures) in the small intestine. The capsule endoscopy is a camera pill that you swallow and it takes 2 pictures per second as it travels through your small bowel; this is helpful for some people in determining whether they have small-bowel Crohn's disease. The CT scan is helpful in identifying abscesses or fistulas that often accompany inflammatory bowel disease. The abdominal ultrasound looks at the gallbladder, pancreas, kidneys, and liver to check for enlargement, stones, etc.
Sometimes the whole work-up will be completely negative. It's frustrating, but there are many, many people in the same boat. Medical science hasn't figured out every single little thing that can go wrong in the body and if they can't find the culprit, there is really nothing the doctors can do except treat the symptoms. They can't treat something they can't see, because the drugs they use can be very harmful if used incorrectly.
Your doctor, though young, sounds like he is working with you, and there is a lot to be said for that. Young docs are often much better to work with in these cases because they are willing to do a little more research and they have more energy; plus, he probably really is in medicine to help people and not get rich, since medicine is changing so drastically these days and docs really aren't getting paid as much as they used to be, or should be (you should see the amount of work, money, and soul they have to pour into the institution to get that degree!).