It sounds like Separation Anxiety to me. I went through this with one of my bitches and it really is something that you need to talk with a behaviourist about. There is no easy fix for SA and it really is a long road that requires A LOT of patience and understanding on the part of the owner.
Like your dog, my bitch peed and pooped her crate each and every time we left the house, even if for only 20 minutes. It was very frustrating and at times, we felt like prisoners in our own home. We were finally able to over come it, but it took a full year of behaviour modification to do it.
I also highly recommend Patricia McConnell's book called, "I'll Be Home Soon". It is a cheap book at around $10 and it will help you to understand what is going on with him.
Here's a link to a site that you can order it from: http://www.dogwise.com/itemdetails.cfm?ID=dtb667