So very sorry to hear of your problems with which I can entirely sympathise. I have had Crohn's for the last 37 yrs and have had my share of flares. However, I got breast cancer in 2003 and had to stop my normal medication (methotrexate, which is an immuno-suppressant chemo) in order to have FEC chemo. For 4 months I didn't eat any solid food. I existed on hospital prescribed Frutijuice, 3 cartons a day, 300 calories each. I still had to wear incontinence pads when I went out, usually just to the hospital by car for my chemo, but still had faecal incontinence in the street, so I know where you are coming from.
I would think you need to see a gastroeneterologist as your incontinence may be caused by ulcerative colitits, or Crohn's. It looks as if a parasitic infection has been ruled out by stool culture. It may be just coincidental with ovarian cancer, of which I know nothing. The only way to definitely diagnose inflammatory bowel disease is through a lower colonoscopy, or an upper endoscopy, with biopsies. There are some new medications now which are very effective. I self inject 12.5 mg of methotrexate once weekly and this has kept my disease in remission - it is never cured. I still have watery or explosive movements in the early morning, but daily codeine phosphate and Triptofan do help in slowing down my motility. I sometimes have to take Imodium if I have been to the loo 4-5 times in the first hour of rising. I have found these meds the only way I can cope with a reasonable quality of life.
A recent new test, calprotectin stool assay, can identify if you have inflammation in the gastric tract, but not specifically where. It is non-invasive and quite cheap to do compared to the scopes. This could give the gastro the information to proceed with scopes.
I do hope you seek out a good gastroenterologist with experience in treating IBD and that you get some answers, and treatment.