IBS or Something Else??

Hi All,
I am new to this, but excited to get some advice from people who can relate to what I am going through. Heres a condensed version of my story...

I was diagnosed with Ulcerative Colitis in 12/2006 when I was hospitalized with severe rectal bleeding, fatigue and dehydration. In the years since, I have suffered with many flare ups but have never bled again and always been able to get it under control with changing my diet and increasing medication.
Last July, I noticed a change in my bowel habits - thinking it was a UC flare, I changed my diet and increased meds. Symptoms slowly got worse and worse until late November when things got really bad. Frequent loose/soft bms with abdominal pain. I had one week where I was going up to 15-20 times, then slowly went down to 4-6 then out of no where would go up again. In December I had a endoscopy and sigmoidoscopy that were normal, went on the SCDiet, had small improvement but had bad days and ok days. My Dr. said I am fine and did not offer any other suggestions. In January I went to another Dr. and had a colonoscopy which showed my UC was "mildly" active but not the cause of my symptoms. I had a Cat scan and did the SIBO breath test which were both normal. I was told it could be IBS and was prescribed Rifomaxin which did not do much.

I kept a food journal and couldn't seem to find a link or pattern. Although, seemed like things that were high in fructose caused a lot of "bubbling" loud, movement on the right side of my abdomen. I took probiotics and stayed on the SCDiet. I thought I was on the road to recovery until I got very sick again in March, going to the BR up to 20 times a day with rectal bleeding (that may or may not have come from hemorrhoids or a fissure). A new Dr. said it could be the UC and prescribed a low dose steroid, canasa and increased my Asacol HD to 9 a day with not much improvement. Then, I tested positive for C-Diff and went on Flagyl. (The only time I was in a hospital and was on a lot of antibiotics was in 2007 when diagnosed with UC and have never been in contact with anyone that has C-Diff!) I got better but still had GI problems, loose BM's 2-6 times a day.

about 2 weeks ago, I started having similar symptoms to when I tested positive for C-Diff. I recently went to the ER with severe pain and frequent BM's that were loose but not watery. They gave me fluids and when it finished, I got a bad attack again. I was put on fluid Flagyl and morphine. Not knowing IF this is the C-Diff again or not, I was taking Flagyl for the past 3 days. But stopped because of 2 stool test came back negative. I am extremely weak, I wake up multiple times in the night, going 10-12 times a day, any movement triggers a BM with pain. This is probably a side effect of the flagyl (that I did not experience with the first round) but I now have legit watery diarrhea. My doctor today said that IBS usually doesn't wake you up at night for BM's and going to the BR this many times with this much pain.
He also told me to take Imodium and if that does not work that I may just need to deal with it.
All my blood work has always been pretty normal since this all started. I don't think this is IBS but I can not imagine what else can be causing this.
Now and before this, my diet is mostly just protein. Barely any fruits or veggies because I was always scared of what they would do to me, am I now suffering because of this? Could this just be a severe imbalance in my gut flora or is it something more serious?
On a side note, I also found out that I have a simple ovarian cyst of 4mm. Is there a link?
I am a 26 year old with absolutely no life and am quickly losing hope of ever having one. I need help badly! What is going on inside me???
Has anyone experienced anything like this with IBS?
(so sorry for the lengthy post)