I just thought I'd update this. The Entocort gave me the push that I needed to get better. I know I'm not at 100% yet, but I'm definitely on the right track.
I did have one problem with the Entocort though. The little shells of the balls of medicine inside the capsule gave me trouble. A few times I had some trouble where transit time was increased and I narrowed the problem down to these little shells passing so fast through my tract that they were basically giving me brush burns in my rectum.
When my transit time would increase for other reasons, I'd have to back off of the Entocort some. I'm not down to 2 pills a night instead of 6 a day. It is a much better balance. It may be slowing my recovery, but I'm able to manage everything else better.
The only other problem that I am having is that when I eat some fiber and have more formed stools, I still have pain as it passes through the terminal ileum. I believe this is from slight thickening of the intestinal walls that I have. It's actually seeming to be a little better to eat where I'll have softer stools to keep the pain away.
I know it's TMI, but really, do any of us have any shame on this topic anymore?