I agree. There is no telling what kind of life he had before you got him and since cats are prone to having human ailments, I wouldn't be surprise if he has IBS (irritable bowl syndrone).

I have lived with that for over 30 years and stress is one of the key factors. Life on a even keel is what keeps it under control. He could have thought he was being punished for something and uspest that he didn't know what...

It will take a long time for him to fully trust another human but he will, in time. One day at a time, one step at a time, in HIS own time...