Hopefully now that you have this diagnosis they will be able to finally treat the correct disease. There are others here that have faced the Crohn's diagnosis after getting their j-pouches. I had many of your same problems, like c.diff and pouchitis, and my j-pouch ultimately failed. It had to be removed. My medical "choices" were like choosing between evils similar to which I image you are now faced with.
I feel for your pain and feelings of hopelessness. Please don't give up.