A couple of things I've learned the hard way during the last 10 years: 1. It's best not to change more than one thing at once, and 2. Even if the foods seem to be the same, they may not be tolerated in the same way. I also agree with greysmom's comment that it's not necessary that the food be a prescription diet, only that it be tolerated.
I don't have experience with the neurological issues (at least, not the ones you're facing), but I'd be inclined to revert to the previous diet and meds until he's stable, then try altering (reducing or exchanging) the metronidazole. If you can keep him stable, then you might try switching his food.