Years ago when I worked in labs Charcot Leyden crystals were often associated with Endamoeba hystolitica altho the list of parasites, usually protozoa has grown. I have read newer research and treatments need to include digestion of the biofilm which protects these organisms from what is used to treat them, meds or herbs. It seems that the onset was rather sudden which would indicate the problem started with a bacterial infection. Usually parasites take up to two weeks to cause symptoms. You had exposure to both.
Another suggestion is that the infections triggered Celiac Disease. The stool test your ordered may include a test for this gluten sensitivity, usually an anti gliaden antibody test. Metametrix Lab enteric panel includes this test.
There are several alternative programs for healing the bowel, Two of the most effective are Hulda Clark 's and Dr. Bob Schultze's. Much of Schultze's treatments can be found by going to the Schultze Forum.