I am glad you finally have a diagnosis, and it's not the unmentionable! Fletcher has fairly mild IBD, and once I figured out what his triggers were, he has not had to be on any regular meds. Beau's is more severe, it sounds like, and he may need some form of meds all his life, but at least it can be managed!
It will take some time, and you'll have to watch his diet like a hawk, once you figure out what works (and what doesn't). There are a variety of supplements that can help, Fletcher gets pumpkin and yogurt with every meal. He was on colostrum for awhile at the beginning, too. I would hold off on these though, if it were my dog, until you have his main food source worked out.
I am adding this after reading your latest email. Remember that he probably still doesn't feel 100% from his surgery, and he's not a morning person when it comes to eating The pred should work pretty fast, but it still may take a couple of days. more