This is from a Doctor in MN that responded to my request
I am sorry to say, but we do not have a protocol to perform fecal bacteriotherapy for ulcerative colitis. The procedure is only offered to patients with recurrent, refractory C. difficile infection. Your idea is reasonable, and in 2003 Dr. Borody in Australia has reported a few patients with UC who benefited from bacteriotherapy, but they haven't published anything new since on the question.
We are currently considering setting a protocol for a non-C. difficile indication, and perhaps more will follow. But, we will need to take things in the proper order, e.g., IRB approval first, setting up data monitoring board, etc. However, I have to stress that there is still essentially no data to suggest this will work for UC. It is established that colon flora is different in UC compared to normals, but personally I think that is the consequence of disease rather than the cause.
For what it is worth, I treated three patients with refractory C. difficile colitis and underlying Crohn's disease. Their C. difficile infection was treated, but their Crohn's didn't go away.
If you're having terrible rectal pain, you should have a careful exam for an anal fissure. Prednisone is only a temporary crutch in management of IBD. However, you may actually need an immunomodulator drug like azathioprine or 6-MP.