When Spencer had similar neuro issues, it was before the IBD was even diagnosed. He had it, just not diagnosed yet. Intestinal Malabsorption was the diagnosis after the neuro issues, and B-12 shots put a stop to them. He still gets them every two weeks because that's the frequency that works best for him. At the beginning it was twice a week. But, yes, he had a lot of trouble getting up, he'd about fall over when lifting a leg to pee, and he got confused about where he was and what he had wanted to do when he got there! That cleared up immediately with the B-12. It's such a simple but neurologically critical thing.
He started Flagyl in early '09 and was on it continuously for two years. But we got the dose down to 250 mg. twice a day, then once a day, and for the last year or so only give it for a day or two at a time when he has a flare. We do give him 1/8 tsp of tylosin twice a day, and for the most part that does the trick.
We also have all this time used budesonide as an immunosuppressant, starting at 3 mg/day and working our way down to what it has been for the last 9 months or so, 1/2 mg. every third day.
Not only did we need a novel protein for meat, but we had to eliminate all carbs except sweet potato. So we use Natural Balance kibble, along with Wellness canned, and he has never used a prescription food at all. That's because the prescription foods seem to be heavy on rice, or corn, or both, neither of which he can handle at all. (He could have anything but white rice before the IBD, but no grains at all since then.) Talking with AJ Hicks and others here on GT gave us the idea that many of these IBD dogs need foods that minimize carbs, and that approach has worked very well for us.
I'm so sorry Merlin is having this trouble, and I know how hard it is on you too. We'll keep you in our thoughts and hope you can turn this around.