[Dreamer74]

I am wondering if he has too much freedom. I would suggest keeping him in a small area with a bed, food, peepads when you are gone. Make sure that before you let him out into the rest of the house that he uses the pee pad or goes outside. I always gave treats and lots of praise. Then take him back there every couple hours to make sure he goes, if he won't leave him back in that area.
I have never used the crate as punishment, just because I want to love it and be happy in it and not think of it as punishment.