Digestion is the CORE of health. That is something I have learned first hand. Some of what you say reminds me of hypothyroidism, but I think #1 has to be optimizing digestion.
If I were you I'd jump on Humaworm and DE and see what comes out... lol, at least if nothing does you can rule out parasites.
Psyllium seed husks and water will help "keep things moving".
It could very possibly be a liver issue. Getting a good daily dose of malic acid, choline(+inositol if you want) and sulphur (garlic, MSM, etc) will help to purge any fat out of it, as well things like Liver Flushes or lemon juice.
Bacteria is another possibility, if a less likely one. I am mainly looking at Colloidal Silver (and zappers) as I think my problems may be down to bacteria. Brocolli seed extract (sulforaphane) is good for h. pylori, but I don't know if it's likely to be that in your case.
Other than that... lots of nutrition and exercise, maybe a liver-healthy supplement like the one on the Humaworm site (I also hear good things about liv52 but I don't know anything about it first hand). A colonic or Oxypowder may help to purge the intestines.
Sorry if that overwhelmed you, that's just the best stuff I can think of right now :)