If it is separation anxiety, you might also want to leave a piece of your clothing behind (that you don't mind getting chewed or dirty!) in the crate for him. I crate trained Baxter, actually still am, and he has never to this day peed or pooped in his crate. I always try and leave a chew toy and/or a piece of my clothing. I heard/read somewhere that they like the scent.
Good luck though!
