I also agree with not crating him if soiling in the crate occurs...why add more stress? It's still sounds like SA if it's not medical and that's where I would concentrate my efforts. I'd also seek out another vet, just for a different opinion. However, I wouldn't mention your current vet's diagnosis (or lack of It), I'd just see what another vet has to say about it.
Good luck, and hopefully you can get this figured out soon because it isn't normal behaviour.