I don't have a lot of time at this very second to respond to your post in detail, but I wanted to let you know that I too have had a VERY bizarre case for the past several years - cyclical periods of watery diarrhea, fevers, weight loss, etc. - after living in East Africa for a few months, where I had contracted amoebic dysentery. The U.S. labs have never recovered any parasites from my stools, however, and even though I've had "markers" of infection (leukocytosis and fever) there has been no definitive answer about what these episodes actually are.
One question - have you ever been on metronidazole (Flagyl) and/or ciprofloxacin (Cipro)? These drugs have been the MOST effective for me in reducing my symptoms; I've taken them on several different occasions and usually feel better for a few months afterwards.